Robert Castelo
| Snapshot Date: 2025-11-13 13:40 -0500 (Thu, 13 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/GSVA |
| git_branch: devel |
| git_last_commit: 13f832d |
| git_last_commit_date: 2025-11-12 08:34:40 -0500 (Wed, 12 Nov 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-14 11:36 -0500 (Fri, 14 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4825 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4547 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 932/2325 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GSVA 2.5.6 (landing page) Robert Castelo
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the GSVA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GSVA.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: GSVA |
| Version: 2.5.6 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GSVA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GSVA_2.5.6.tar.gz |
| StartedAt: 2025-11-13 20:21:49 -0500 (Thu, 13 Nov 2025) |
| EndedAt: 2025-11-13 20:24:26 -0500 (Thu, 13 Nov 2025) |
| EllapsedTime: 156.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: GSVA.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GSVA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GSVA_2.5.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/GSVA.Rcheck’
* using R Under development (unstable) (2025-11-04 r88984)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.8
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GSVA/DESCRIPTION’ ... OK
* this is package ‘GSVA’ version ‘2.5.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GSVA’ can be installed ... OK
* used C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’
Running ‘test_gsva_newapi.R’
Comparing ‘test_gsva_newapi.Rout’ to ‘test_gsva_newapi.Rout.save’ ... OK
Running ‘test_plage_newapi.R’
Comparing ‘test_plage_newapi.Rout’ to ‘test_plage_newapi.Rout.save’ ... OK
Running ‘test_ssgsea_newapi.R’
Comparing ‘test_ssgsea_newapi.Rout’ to ‘test_ssgsea_newapi.Rout.save’ ... OK
Running ‘test_zscore_newapi.R’
Comparing ‘test_zscore_newapi.Rout’ to ‘test_zscore_newapi.Rout.save’ ... OK
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
GSVA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GSVA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’ * installing *source* package ‘GSVA’ ... ** this is package ‘GSVA’ version ‘2.5.6’ ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.1.sdk’ clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/cli/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ecdfvals.c -o ecdfvals.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/cli/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c kcdfvals.c -o kcdfvals.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/cli/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c kernel_estimation.c -o kernel_estimation.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/cli/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ks_test.c -o ks_test.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/cli/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c register_cmethods.c -o register_cmethods.o clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/cli/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c utils.c -o utils.o clang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o GSVA.so ecdfvals.o kcdfvals.o kernel_estimation.o ks_test.o register_cmethods.o utils.o -F/Library/Frameworks/R.framework/.. -framework R installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/00LOCK-GSVA/00new/GSVA/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GSVA)
GSVA.Rcheck/tests/runTests.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> oldWarnOptionValue <- options(warn=1)
> BiocGenerics:::testPackage("GSVA")
Running unit tests for input gene sets.
Running unit tests for GSVA C code without missing data.
Running unit tests for GSVA C code with missing data.
! Input expression data has NA values, which will be discarded from calculations
Running unit tests for GSVA ranks.
Running unit tests for input data containers.
ℹ No assay name provided; using default assay 'counts'
ℹ 300 nonzeros (less than 2^31) and 0.00% sparsity
Running unit tests for the new API.
Running unit tests for gsvaParam.
Running unit tests for plageParam.
Running unit tests for ssgseaParam.
Running unit tests for zscoreParam.
Running unit tests for sparse methods.
ℹ 100 nonzeros (less than 2^31) and 0.00% sparsity
Running unit tests for ssGSEA.
RUNIT TEST PROTOCOL -- Thu Nov 13 20:23:55 2025
***********************************************
Number of test functions: 11
Number of errors: 0
Number of failures: 0
1 Test Suite :
GSVA RUnit Tests - 11 test functions, 0 errors, 0 failures
Number of test functions: 11
Number of errors: 0
Number of failures: 0
> options(warn=oldWarnOptionValue[["warn"]])
>
> proc.time()
user system elapsed
5.716 0.239 6.331
GSVA.Rcheck/tests/test_gsva_newapi.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
> ## 2025-11-12 regression test script for method GSVA
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(geneprotExpCostaEtAl2021)
>
> set.seed(2025-11-12)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 -0.1065910 0.076987224 -1.3963246 1.2771019 -0.3372823
g2 1.6144451 0.006987175 1.2139285 0.9773345 0.2874821
g3 1.3882628 -0.690659025 -2.0385616 0.2804193 -0.1822753
g4 0.7027778 0.562919910 -0.1736422 0.3117396 0.3527060
g5 2.2575002 0.199992976 -0.4118118 0.1876944 0.2664025
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> gsvaPar <- gsvaParam(X, gs)
> gsva.es <- gsva(gsvaPar, verbose=FALSE)
> dim(gsva.es)
[1] 100 30
> gsva.es[seq.int(min(nRowsToPrint, nrow(gsva.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 -0.022997477 -0.202142718 0.236559185 0.302618715 -0.3667588315 0.09182160 -0.20878577 0.11025341 -0.23129598 -0.070082207 -0.145395460 -0.24105583 -0.448182220 0.12623472 0.0937507470 0.127584309 0.34942965 0.26747008 0.070475368 0.110558646 0.271154751 0.070557193 0.008436268 -0.16958768 0.07770511 -0.136229484 0.2224517839 -0.114832694 0.260581800 0.072693549
gs2 0.069867909 0.129540545 -0.060113080 0.143511820 -0.0009722817 -0.04966520 -0.16134297 -0.17684957 0.15335495 0.118906704 -0.014989066 0.08696776 0.170284102 -0.02331696 -0.0174106236 -0.074952426 0.02623157 -0.18928650 0.257209515 0.025480254 -0.089623748 -0.218311238 0.199852651 -0.13212324 -0.15559612 -0.046389250 -0.2134350205 0.006094199 0.219320594 0.227708520
gs3 -0.005692873 0.105805842 -0.066465400 0.082881540 -0.1567357941 0.18641567 0.16533784 0.11245608 -0.16995510 0.122769505 -0.035003594 0.13598712 -0.180397994 0.04307524 0.0113280610 0.059802742 0.02408661 -0.08040934 0.133406330 -0.002731046 0.052838952 -0.038848936 0.114406098 -0.05804139 -0.10660743 -0.214242288 -0.0598103770 0.046330894 -0.151903420 0.020232767
gs4 -0.160422981 0.038974885 0.250364253 -0.002212993 -0.0351733262 -0.03804557 0.12590000 -0.10557022 -0.02850232 0.049293279 -0.048104593 0.17044886 0.098128303 0.10983169 0.0463499169 0.009393574 -0.09648566 0.05525000 0.177279376 -0.092800011 -0.101217627 -0.142820062 -0.144930151 0.06356258 -0.08300004 -0.053411837 0.0632674297 -0.063772291 -0.027314484 0.005586407
gs5 0.045202437 -0.003740420 0.077031610 -0.192101809 0.1414148290 -0.04416954 0.03598764 0.15545034 -0.13146568 0.025711790 0.039068485 -0.10698156 -0.134740147 -0.09885333 -0.0758862432 -0.152333469 -0.03265945 -0.06661855 -0.207737815 -0.011095528 0.228545399 0.166392944 0.156445402 -0.07371989 0.23541664 0.113305551 0.1022646864 -0.302796335 -0.031734769 0.183577614
gs6 -0.101151401 0.095213746 -0.202205735 0.041599623 0.2215711751 0.13112930 -0.18496741 -0.02546188 0.07457682 -0.187008192 -0.098862358 -0.08671122 0.255902152 0.13863946 -0.0672815563 0.040189189 -0.23984863 0.02273628 0.176776316 0.202849152 0.022054822 0.023278263 0.131991785 0.13109638 -0.05194763 -0.178734047 0.1817840250 -0.016159540 -0.286773044 0.049272908
gs7 -0.141856825 -0.160624372 0.004760558 -0.024365232 0.0422434510 -0.11059554 -0.11970851 0.15251742 0.01262721 0.022722004 0.123133382 -0.09991274 -0.213892560 0.14470421 -0.0246648437 -0.022230236 0.08510422 -0.26443232 -0.019964148 0.225362344 -0.176647811 0.120566985 -0.081382371 0.08927098 -0.08294746 0.068768121 0.1797758087 0.234709921 -0.007318997 0.088985502
gs8 0.113841163 0.015418935 -0.052795084 -0.019472928 0.0820348388 -0.24934626 0.17529399 -0.16094070 0.12853497 -0.067610136 0.001555347 0.29197372 0.118815328 -0.03800041 0.0142031745 -0.048858030 -0.13102299 -0.12455151 -0.129074238 -0.065214046 0.003182421 -0.107092369 -0.001123296 0.01101381 0.14924107 0.106849420 0.0126276030 0.018928311 -0.032765082 0.024795457
gs9 0.038281116 -0.165886734 -0.204890471 -0.133155197 0.1653707655 0.01046597 0.06314466 0.06031654 0.20822926 -0.109030347 -0.067151045 0.09649805 0.047717505 0.05832707 0.0193917430 0.113862907 -0.05384893 -0.07706778 -0.018847127 -0.066498915 -0.101182067 -0.214444871 -0.076776431 0.13093044 0.26497481 0.234899236 -0.0910052384 0.035421031 -0.091450797 -0.051681202
gs10 0.117102328 0.082532073 0.022627242 0.078615309 -0.1142884441 -0.02556677 0.15796952 -0.16627553 -0.11682631 0.081618913 -0.214831429 -0.06155837 -0.055477883 -0.14210355 0.0978880116 0.017871997 -0.09691630 0.05407352 0.005671711 -0.003655329 0.078825162 0.125739459 -0.007014561 0.13185612 -0.01465023 -0.041961032 -0.0623881904 -0.047691194 0.236607060 -0.142177003
gs11 -0.168019157 -0.151797753 -0.032873837 0.194497938 0.0775012481 -0.01857060 0.20497131 0.03743947 0.03901438 -0.229879580 -0.089673842 0.05696191 0.041045442 -0.05746124 0.1438863991 -0.180644481 -0.15231074 -0.14444996 -0.043005146 0.230828119 -0.155159190 -0.081260183 0.145331734 0.13824027 0.17790392 -0.026122482 -0.1167696333 0.151205380 -0.054133379 0.138727113
gs12 -0.007133371 0.190151096 0.019314460 0.113893577 -0.0807523116 -0.16903421 -0.01061067 0.05459171 0.20836170 0.089806258 0.193052974 -0.21805806 0.260938778 -0.02751492 0.0417304293 0.208240540 0.18566054 0.02542285 -0.399501071 -0.235840902 0.170032509 -0.095330108 -0.236900628 -0.16957336 -0.07697002 -0.168952069 -0.0738858644 -0.037115971 0.145333309 -0.072691633
gs13 0.039746033 -0.279152173 0.257603597 0.169233512 0.0373025812 -0.05006644 -0.05995272 0.02288368 0.01875307 -0.157231453 -0.156796981 0.07050044 -0.149265242 0.16449331 -0.1937488294 -0.149406312 0.12228291 -0.05060087 -0.153797841 -0.141271942 0.100859578 -0.002107204 0.053999687 0.17638951 0.37084768 -0.051866110 0.1720479747 -0.179297943 -0.025750564 -0.015477176
gs14 -0.152730065 0.034902064 -0.064138685 -0.102173170 0.0394503879 0.09239308 -0.20959342 -0.04739496 -0.03517519 0.079916985 -0.132564949 -0.04121974 0.075270260 -0.16928655 0.0185585377 -0.167741683 0.09070753 0.08699991 0.015315905 -0.048876997 -0.130304646 0.082002957 -0.023719147 -0.07057306 0.25589870 0.247160158 -0.0812581220 0.174949046 0.096486548 0.087754978
gs15 -0.277833817 0.084745625 -0.409285312 -0.020350508 0.0839877297 0.55413746 -0.04487033 -0.25907919 0.16739458 -0.039727701 -0.049747425 -0.30726467 -0.462502907 0.35685086 0.1741838068 0.277882528 -0.08081222 0.28682981 -0.152192842 0.045494109 -0.220650121 0.165896142 -0.504631438 -0.00572512 -0.10089246 0.075125322 -0.1572093758 0.198526858 0.101285078 0.320235074
gs16 0.237158974 -0.173149678 0.021363917 0.035582956 0.2204774471 0.22272407 -0.23282325 -0.14609479 0.37512052 -0.002855036 -0.162588064 0.05010286 0.114667706 -0.33644745 -0.2364818132 -0.184512832 -0.02255019 -0.20839040 0.258272116 -0.164074283 -0.238867604 0.133860083 -0.036983976 0.21926004 0.08077769 0.249452640 0.3228915911 0.205431195 -0.226034372 -0.173309566
gs17 -0.027068242 0.051128005 -0.108010899 0.004985785 0.0458305229 -0.02964526 0.23718028 0.02614311 0.03474876 -0.080939249 -0.115192450 0.01643314 -0.216256946 0.09553137 0.0715385266 0.136432982 0.02070642 -0.07510087 -0.055183509 -0.025526468 0.066359273 -0.197134600 -0.049197816 0.13981030 0.01418391 0.001367496 -0.1214089383 0.015141188 0.097189951 0.048064119
gs18 0.006293873 -0.250818099 0.156735899 0.026459860 -0.1507611125 0.13443796 -0.07405618 0.04150140 0.01305453 -0.050509914 0.180376201 -0.17806029 0.035950153 0.24646253 -0.0611268357 -0.086986151 0.08285188 -0.08486543 0.092150612 -0.027559359 -0.019662346 0.036535506 -0.004766760 0.11380847 0.15064651 -0.079696172 -0.2144617867 -0.102143615 -0.016738307 0.151734350
gs19 -0.011962872 0.148884106 0.172978324 0.008851502 -0.1344591502 -0.15321457 -0.13026230 0.09133253 0.02969258 0.006525593 -0.045096922 -0.13281822 0.003588889 -0.09317708 -0.0004644248 0.037899526 0.10449308 0.16926297 -0.019638916 -0.151556777 -0.079720887 -0.016922856 0.018781682 -0.04479470 0.04371368 -0.098423232 -0.0629933453 0.201222233 -0.058424097 0.074230077
gs20 0.081926772 0.147840168 -0.064225313 0.232971348 -0.0665485504 0.18562614 -0.18746820 0.34589993 -0.32489203 0.193083287 0.013994533 -0.11965054 0.361474739 0.10428509 0.2300003886 -0.303648844 -0.33014527 -0.23249305 -0.282767577 0.359950593 -0.194890083 -0.266857343 0.231400572 -0.15819845 0.47178213 0.016717262 -0.1215259566 -0.028401093 -0.136560883 0.007006979
gs21 -0.045749121 -0.232712508 0.098244084 -0.225121889 -0.0134956529 0.24888039 0.34623385 0.18234198 -0.04490438 -0.066319128 -0.091485995 0.14105698 -0.084746912 -0.11132745 0.2510922385 -0.162574014 0.19193238 -0.14846453 0.382788683 -0.023392427 -0.305446080 -0.165393307 -0.374271129 0.09649475 -0.13426507 0.477871640 -0.0621464627 -0.138043968 -0.030890202 0.018796230
gs22 -0.237412025 0.006447096 -0.133865502 0.092070223 0.3746959238 0.17166986 -0.20739838 -0.18006241 -0.09761431 0.068458890 0.101833580 0.20736905 -0.194239535 -0.15737467 0.3344891359 0.190461406 -0.02203098 0.01359537 -0.096586415 0.142655186 -0.099266615 -0.131308533 -0.217519398 -0.32815831 -0.18091395 0.187266495 -0.1299962008 -0.144607465 0.283242500 0.176010459
gs23 0.190415312 0.077045218 0.122323140 0.225229531 0.0556437464 -0.08775647 -0.16727916 0.11798887 -0.01640574 -0.325178292 -0.028746497 -0.25266300 0.220087684 0.12866805 0.2386309465 -0.006614818 -0.30618281 -0.06980429 -0.063318773 0.158561562 -0.156266247 0.030558285 0.217438213 -0.16296449 0.01826912 0.183386259 0.0006773755 -0.050222694 0.011216649 -0.175566800
gs24 0.281822947 -0.250097132 0.276328378 -0.029504134 0.1705584222 -0.33107919 -0.28475345 0.20772600 0.23970926 -0.173997125 -0.441664514 0.10765028 0.195604602 -0.26390827 0.0056296087 0.303057626 0.23985623 -0.23495701 0.465436703 0.096252597 0.054463039 -0.069266265 -0.140740502 -0.13513410 -0.30892914 -0.141877998 0.0032713565 0.248883512 0.473396607 -0.585334293
gs25 0.199849556 0.141623686 0.025047784 -0.110660348 0.2828871008 -0.16169462 -0.28000309 0.23087492 0.37226210 0.187384149 -0.103480250 0.08546276 -0.072181686 -0.02832541 -0.2666116623 0.135112853 -0.12080019 0.30450320 -0.177333096 0.009902668 0.362160182 -0.234464127 -0.053308631 0.01445325 -0.20487586 -0.070595577 -0.2188882525 -0.334186099 0.133468658 -0.029316084
>
> c2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> firPar <- gsvaParam(geneExpCostaEtAl2021, c2BroadSets,
+ minSize=10, maxSize=500)
ℹ No assay name provided; using default assay 'logCPM'
> fir_es <- gsva(firPar, verbose=FALSE)
> assay(fir_es)[seq.int(min(nRowsToPrint, nrow(fir_es))),]
BS03 BS04 BS05 BS06 BS07 BS08 BS09 BS10 BS11 BS12 BS13 BS14 BS16 BS17 BS18 BS19 BS20 BS21 BS22 BS23 BS24
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP 0.02292349 0.12790635 -0.179968777 -0.53107430 -0.659537438 0.45203899 -0.61015343 -0.1413142628 -0.117777932 -0.596835693 0.615435856 0.274946146 -0.41524421 0.39705826 0.35202338 0.050135781 0.257858640 -0.11515971 0.403840241 0.173064103 0.107755544
WINTER_HYPOXIA_UP -0.23987162 -0.12604006 -0.264481894 -0.34346399 -0.397820755 0.23863858 -0.37508089 -0.1335252981 -0.140217740 -0.331601104 0.376283515 0.150845377 0.13023159 0.40599546 0.11528435 -0.009480635 0.053639096 -0.04637949 0.129361851 0.280773073 0.124585543
PARENT_MTOR_SIGNALING_UP -0.01023211 -0.06240698 -0.030713760 0.02678851 0.080531564 0.05423200 0.20395415 0.0271645985 -0.074859366 -0.121317727 -0.099664851 -0.015265185 0.24736481 -0.05285336 -0.16909890 0.070570578 -0.142717585 0.05791113 -0.061313455 -0.024164966 0.014347801
PYEON_HPV_POSITIVE_TUMORS_UP 0.42809640 0.32919003 0.389812309 -0.23278421 -0.209862906 0.09824133 -0.03337240 -0.0607003970 -0.087846994 0.235249450 0.483921506 0.490407343 -0.45257194 -0.38786274 0.15933512 -0.388410321 -0.079215650 -0.22919078 0.115369167 -0.320680827 -0.214079223
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP -0.22750351 -0.22105325 -0.220566467 -0.23490878 -0.364982300 0.12748621 -0.31660045 -0.2139208866 -0.077340363 -0.280979075 0.340735303 -0.087198822 -0.18556247 0.28045230 0.23061930 0.065292446 0.344365500 -0.05134999 0.290138193 0.177470287 0.191859158
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP -0.04740536 0.13150260 -0.302637019 -0.43573567 -0.318388023 -0.29419293 -0.48476141 -0.1708234516 -0.182700833 0.194991420 0.096775852 0.237990325 0.22775317 0.36197706 0.30931300 0.231695063 0.427179760 -0.27098592 -0.083034580 0.368102049 -0.005283552
LU_TUMOR_VASCULATURE_UP 0.22404058 -0.43068932 -0.380600990 0.00236026 0.403950738 -0.09003451 -0.01835083 0.3843713085 -0.034318792 -0.116724831 -0.118200373 -0.181063134 0.37337536 0.00870954 -0.14415171 0.204612942 0.047958533 0.25389697 -0.260712417 0.268384677 -0.267685714
KORKOLA_EMBRYONAL_CARCINOMA_UP -0.04757007 -0.13586445 -0.015447279 -0.50293007 -0.317759661 0.32009785 -0.21377110 -0.2204992126 -0.300076046 -0.138708479 0.420072650 0.124466541 -0.39289128 0.12430012 0.27351406 -0.050506340 0.009461887 0.15557721 -0.079901700 0.327628019 -0.107037370
KORKOLA_TERATOMA_UP 0.46808925 -0.21774496 -0.129682230 -0.39264679 -0.167144223 0.28184319 -0.05816003 -0.2609695799 -0.407058033 0.198844987 0.380908468 -0.090724169 -0.16662244 0.20265846 -0.05412133 0.165060786 -0.061931872 0.35737410 -0.455072189 0.381135317 -0.359773912
KORKOLA_YOLK_SAC_TUMOR_UP -0.16725651 -0.32974789 -0.221800018 -0.48932131 -0.291849820 0.46380803 0.14096780 -0.3865711938 -0.246921657 0.029436052 0.507668708 -0.390282917 -0.51252806 0.21846725 0.37842724 0.023720864 -0.092246760 0.15931049 0.095770965 0.104958264 -0.005095761
KORKOLA_SEMINOMA_UP -0.33562601 -0.28577523 -0.244262534 -0.27800506 -0.069626946 0.32309291 0.08800900 0.0833321577 -0.277191117 -0.099837165 0.282453492 -0.070222343 -0.17513989 -0.01922153 0.05170892 0.329496921 0.138561508 0.14092981 -0.002493429 0.053117518 0.053180172
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP -0.13542260 0.01515806 -0.123710830 -0.15957938 -0.237492560 0.14501130 -0.13338964 0.0572202135 -0.157555272 -0.199427137 0.171315517 0.037788294 0.02258918 0.17076255 0.04897513 0.047182015 -0.054374996 0.23834963 0.018756689 0.256962429 -0.162120270
HOLLMAN_APOPTOSIS_VIA_CD40_UP -0.24952223 -0.22839170 -0.092161117 -0.16513503 -0.228507521 0.15712578 -0.15105318 -0.0007263272 -0.071743015 -0.176708052 0.200717794 -0.060398110 -0.05507417 0.19556884 0.04617003 0.065839300 0.104399289 0.18240655 0.140670149 0.128078917 0.072507958
LIU_PROSTATE_CANCER_UP -0.02530084 -0.28474420 -0.090962845 -0.15503327 -0.148791565 0.24033366 -0.17933889 -0.1445612875 -0.075385781 -0.196033206 0.363058430 0.008430018 -0.08565603 0.08754343 0.11658537 0.027572962 0.093348848 0.08589327 -0.015661941 0.244827565 0.073507178
LIU_SOX4_TARGETS_UP -0.02406433 0.24699598 -0.065885979 0.10154221 -0.122249335 -0.20916134 -0.23055224 -0.0055330354 0.085508371 -0.004532314 -0.150064113 0.122063045 0.00522460 0.22865147 0.15258960 -0.103717219 -0.036804333 0.05202579 0.071969725 0.151502703 -0.145178758
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP 0.21180934 -0.19546723 -0.140082389 -0.10193701 0.005650170 0.05533713 0.06078443 0.0426432072 -0.099630101 -0.006233165 0.128078265 -0.113720741 0.07796755 0.01267864 -0.18849408 0.062068424 0.016825415 0.27151993 -0.176554394 -0.006482359 0.089569220
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP 0.04441846 0.04225478 -0.049898714 -0.13711594 -0.153592793 -0.17120482 -0.40242051 -0.1516006879 -0.170686927 0.229186494 0.032611169 -0.005103335 0.09769941 0.17096206 -0.01281463 0.119646164 0.102260739 0.38260617 -0.238841425 0.449488946 -0.255687685
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP 0.03397928 0.26388388 -0.149410712 -0.07859140 -0.030056165 0.15984260 -0.29834511 -0.3965700456 -0.007409288 -0.174955851 -0.251999452 0.204988714 0.28453515 0.16738681 -0.31311697 0.057903628 0.342199929 0.09401193 -0.006800004 0.092405646 0.134506484
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP -0.38903958 0.09828991 -0.480559229 -0.02241349 -0.155143936 -0.18714452 -0.23277902 0.4840944659 0.365750762 -0.262768901 -0.038041538 0.103290348 -0.28739201 0.24463994 0.12835134 -0.080852874 0.529116082 -0.07419423 0.394703348 0.041489187 -0.279303399
FRASOR_TAMOXIFEN_RESPONSE_UP 0.14513114 0.15204657 -0.011415712 -0.14533939 -0.296185434 -0.03339132 -0.33196505 -0.1347801852 -0.036920881 -0.111410908 -0.075543628 0.046701957 0.11832610 0.15195156 0.10809965 0.055569196 0.071835914 -0.03388644 -0.160697129 0.275314435 0.048533481
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP -0.10766234 0.10322353 -0.364555555 -0.20645899 -0.133541971 0.15573889 -0.21396304 0.0823708144 0.149528954 -0.155237285 -0.007705041 -0.073301722 0.09498367 0.32378661 -0.02198234 0.057138199 0.168222170 0.30591282 0.223683621 -0.063846188 0.109598038
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP 0.27300138 0.17981803 0.005834971 -0.24065397 -0.340627902 -0.07546027 -0.43834122 -0.1917360016 -0.107776808 -0.004744111 0.533808784 0.322443880 -0.45339943 0.08311550 0.34894313 -0.290307573 0.226423203 -0.10026909 0.221255312 0.087976539 -0.259110467
WATANABE_COLON_CANCER_MSI_VS_MSS_UP -0.23657152 -0.18782190 -0.202949000 -0.10513732 -0.497364703 0.36191883 -0.31434211 -0.3891569547 -0.157297886 -0.198849151 0.207380882 0.096259751 0.34514754 -0.23287182 -0.14113604 0.445560091 0.132126827 0.12035394 0.013237341 0.372451838 0.163745844
SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP -0.01857651 0.07156252 -0.204191789 -0.50730032 -0.644390471 0.32055729 -0.56545714 -0.1680683425 -0.273429620 -0.567300383 0.699361412 0.257003106 -0.44168856 0.45577155 0.45041005 -0.269262765 0.250781213 -0.26171756 0.423480829 0.208491300 0.143314032
GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP 0.28776244 0.10484331 0.178368564 -0.05438607 -0.009966795 -0.18753144 -0.17375153 -0.0518374295 0.053535460 0.177138430 0.169801163 0.275453927 -0.15911745 0.06588420 -0.11696977 -0.099197460 -0.157043255 0.27529871 -0.387602857 0.181974900 -0.241074464
>
> proc.time()
user system elapsed
6.521 0.261 7.129
GSVA.Rcheck/tests/test_gsva_newapi.Rout.save
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>
> ## 2025-11-12 regression test script for method GSVA
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(geneprotExpCostaEtAl2021)
>
> set.seed(2025-11-12)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 -0.1065910 0.076987224 -1.3963246 1.2771019 -0.3372823
g2 1.6144451 0.006987175 1.2139285 0.9773345 0.2874821
g3 1.3882628 -0.690659025 -2.0385616 0.2804193 -0.1822753
g4 0.7027778 0.562919910 -0.1736422 0.3117396 0.3527060
g5 2.2575002 0.199992976 -0.4118118 0.1876944 0.2664025
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> gsvaPar <- gsvaParam(X, gs)
> gsva.es <- gsva(gsvaPar, verbose=FALSE)
> dim(gsva.es)
[1] 100 30
> gsva.es[seq.int(min(nRowsToPrint, nrow(gsva.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 -0.022997477 -0.202142718 0.236559185 0.302618715 -0.3667588315 0.09182160 -0.20878577 0.11025341 -0.23129598 -0.070082207 -0.145395460 -0.24105583 -0.448182220 0.12623472 0.0937507470 0.127584309 0.34942965 0.26747008 0.070475368 0.110558646 0.271154751 0.070557193 0.008436268 -0.16958768 0.07770511 -0.136229484 0.2224517839 -0.114832694 0.260581800 0.072693549
gs2 0.069867909 0.129540545 -0.060113080 0.143511820 -0.0009722817 -0.04966520 -0.16134297 -0.17684957 0.15335495 0.118906704 -0.014989066 0.08696776 0.170284102 -0.02331696 -0.0174106236 -0.074952426 0.02623157 -0.18928650 0.257209515 0.025480254 -0.089623748 -0.218311238 0.199852651 -0.13212324 -0.15559612 -0.046389250 -0.2134350205 0.006094199 0.219320594 0.227708520
gs3 -0.005692873 0.105805842 -0.066465400 0.082881540 -0.1567357941 0.18641567 0.16533784 0.11245608 -0.16995510 0.122769505 -0.035003594 0.13598712 -0.180397994 0.04307524 0.0113280610 0.059802742 0.02408661 -0.08040934 0.133406330 -0.002731046 0.052838952 -0.038848936 0.114406098 -0.05804139 -0.10660743 -0.214242288 -0.0598103770 0.046330894 -0.151903420 0.020232767
gs4 -0.160422981 0.038974885 0.250364253 -0.002212993 -0.0351733262 -0.03804557 0.12590000 -0.10557022 -0.02850232 0.049293279 -0.048104593 0.17044886 0.098128303 0.10983169 0.0463499169 0.009393574 -0.09648566 0.05525000 0.177279376 -0.092800011 -0.101217627 -0.142820062 -0.144930151 0.06356258 -0.08300004 -0.053411837 0.0632674297 -0.063772291 -0.027314484 0.005586407
gs5 0.045202437 -0.003740420 0.077031610 -0.192101809 0.1414148290 -0.04416954 0.03598764 0.15545034 -0.13146568 0.025711790 0.039068485 -0.10698156 -0.134740147 -0.09885333 -0.0758862432 -0.152333469 -0.03265945 -0.06661855 -0.207737815 -0.011095528 0.228545399 0.166392944 0.156445402 -0.07371989 0.23541664 0.113305551 0.1022646864 -0.302796335 -0.031734769 0.183577614
gs6 -0.101151401 0.095213746 -0.202205735 0.041599623 0.2215711751 0.13112930 -0.18496741 -0.02546188 0.07457682 -0.187008192 -0.098862358 -0.08671122 0.255902152 0.13863946 -0.0672815563 0.040189189 -0.23984863 0.02273628 0.176776316 0.202849152 0.022054822 0.023278263 0.131991785 0.13109638 -0.05194763 -0.178734047 0.1817840250 -0.016159540 -0.286773044 0.049272908
gs7 -0.141856825 -0.160624372 0.004760558 -0.024365232 0.0422434510 -0.11059554 -0.11970851 0.15251742 0.01262721 0.022722004 0.123133382 -0.09991274 -0.213892560 0.14470421 -0.0246648437 -0.022230236 0.08510422 -0.26443232 -0.019964148 0.225362344 -0.176647811 0.120566985 -0.081382371 0.08927098 -0.08294746 0.068768121 0.1797758087 0.234709921 -0.007318997 0.088985502
gs8 0.113841163 0.015418935 -0.052795084 -0.019472928 0.0820348388 -0.24934626 0.17529399 -0.16094070 0.12853497 -0.067610136 0.001555347 0.29197372 0.118815328 -0.03800041 0.0142031745 -0.048858030 -0.13102299 -0.12455151 -0.129074238 -0.065214046 0.003182421 -0.107092369 -0.001123296 0.01101381 0.14924107 0.106849420 0.0126276030 0.018928311 -0.032765082 0.024795457
gs9 0.038281116 -0.165886734 -0.204890471 -0.133155197 0.1653707655 0.01046597 0.06314466 0.06031654 0.20822926 -0.109030347 -0.067151045 0.09649805 0.047717505 0.05832707 0.0193917430 0.113862907 -0.05384893 -0.07706778 -0.018847127 -0.066498915 -0.101182067 -0.214444871 -0.076776431 0.13093044 0.26497481 0.234899236 -0.0910052384 0.035421031 -0.091450797 -0.051681202
gs10 0.117102328 0.082532073 0.022627242 0.078615309 -0.1142884441 -0.02556677 0.15796952 -0.16627553 -0.11682631 0.081618913 -0.214831429 -0.06155837 -0.055477883 -0.14210355 0.0978880116 0.017871997 -0.09691630 0.05407352 0.005671711 -0.003655329 0.078825162 0.125739459 -0.007014561 0.13185612 -0.01465023 -0.041961032 -0.0623881904 -0.047691194 0.236607060 -0.142177003
gs11 -0.168019157 -0.151797753 -0.032873837 0.194497938 0.0775012481 -0.01857060 0.20497131 0.03743947 0.03901438 -0.229879580 -0.089673842 0.05696191 0.041045442 -0.05746124 0.1438863991 -0.180644481 -0.15231074 -0.14444996 -0.043005146 0.230828119 -0.155159190 -0.081260183 0.145331734 0.13824027 0.17790392 -0.026122482 -0.1167696333 0.151205380 -0.054133379 0.138727113
gs12 -0.007133371 0.190151096 0.019314460 0.113893577 -0.0807523116 -0.16903421 -0.01061067 0.05459171 0.20836170 0.089806258 0.193052974 -0.21805806 0.260938778 -0.02751492 0.0417304293 0.208240540 0.18566054 0.02542285 -0.399501071 -0.235840902 0.170032509 -0.095330108 -0.236900628 -0.16957336 -0.07697002 -0.168952069 -0.0738858644 -0.037115971 0.145333309 -0.072691633
gs13 0.039746033 -0.279152173 0.257603597 0.169233512 0.0373025812 -0.05006644 -0.05995272 0.02288368 0.01875307 -0.157231453 -0.156796981 0.07050044 -0.149265242 0.16449331 -0.1937488294 -0.149406312 0.12228291 -0.05060087 -0.153797841 -0.141271942 0.100859578 -0.002107204 0.053999687 0.17638951 0.37084768 -0.051866110 0.1720479747 -0.179297943 -0.025750564 -0.015477176
gs14 -0.152730065 0.034902064 -0.064138685 -0.102173170 0.0394503879 0.09239308 -0.20959342 -0.04739496 -0.03517519 0.079916985 -0.132564949 -0.04121974 0.075270260 -0.16928655 0.0185585377 -0.167741683 0.09070753 0.08699991 0.015315905 -0.048876997 -0.130304646 0.082002957 -0.023719147 -0.07057306 0.25589870 0.247160158 -0.0812581220 0.174949046 0.096486548 0.087754978
gs15 -0.277833817 0.084745625 -0.409285312 -0.020350508 0.0839877297 0.55413746 -0.04487033 -0.25907919 0.16739458 -0.039727701 -0.049747425 -0.30726467 -0.462502907 0.35685086 0.1741838068 0.277882528 -0.08081222 0.28682981 -0.152192842 0.045494109 -0.220650121 0.165896142 -0.504631438 -0.00572512 -0.10089246 0.075125322 -0.1572093758 0.198526858 0.101285078 0.320235074
gs16 0.237158974 -0.173149678 0.021363917 0.035582956 0.2204774471 0.22272407 -0.23282325 -0.14609479 0.37512052 -0.002855036 -0.162588064 0.05010286 0.114667706 -0.33644745 -0.2364818132 -0.184512832 -0.02255019 -0.20839040 0.258272116 -0.164074283 -0.238867604 0.133860083 -0.036983976 0.21926004 0.08077769 0.249452640 0.3228915911 0.205431195 -0.226034372 -0.173309566
gs17 -0.027068242 0.051128005 -0.108010899 0.004985785 0.0458305229 -0.02964526 0.23718028 0.02614311 0.03474876 -0.080939249 -0.115192450 0.01643314 -0.216256946 0.09553137 0.0715385266 0.136432982 0.02070642 -0.07510087 -0.055183509 -0.025526468 0.066359273 -0.197134600 -0.049197816 0.13981030 0.01418391 0.001367496 -0.1214089383 0.015141188 0.097189951 0.048064119
gs18 0.006293873 -0.250818099 0.156735899 0.026459860 -0.1507611125 0.13443796 -0.07405618 0.04150140 0.01305453 -0.050509914 0.180376201 -0.17806029 0.035950153 0.24646253 -0.0611268357 -0.086986151 0.08285188 -0.08486543 0.092150612 -0.027559359 -0.019662346 0.036535506 -0.004766760 0.11380847 0.15064651 -0.079696172 -0.2144617867 -0.102143615 -0.016738307 0.151734350
gs19 -0.011962872 0.148884106 0.172978324 0.008851502 -0.1344591502 -0.15321457 -0.13026230 0.09133253 0.02969258 0.006525593 -0.045096922 -0.13281822 0.003588889 -0.09317708 -0.0004644248 0.037899526 0.10449308 0.16926297 -0.019638916 -0.151556777 -0.079720887 -0.016922856 0.018781682 -0.04479470 0.04371368 -0.098423232 -0.0629933453 0.201222233 -0.058424097 0.074230077
gs20 0.081926772 0.147840168 -0.064225313 0.232971348 -0.0665485504 0.18562614 -0.18746820 0.34589993 -0.32489203 0.193083287 0.013994533 -0.11965054 0.361474739 0.10428509 0.2300003886 -0.303648844 -0.33014527 -0.23249305 -0.282767577 0.359950593 -0.194890083 -0.266857343 0.231400572 -0.15819845 0.47178213 0.016717262 -0.1215259566 -0.028401093 -0.136560883 0.007006979
gs21 -0.045749121 -0.232712508 0.098244084 -0.225121889 -0.0134956529 0.24888039 0.34623385 0.18234198 -0.04490438 -0.066319128 -0.091485995 0.14105698 -0.084746912 -0.11132745 0.2510922385 -0.162574014 0.19193238 -0.14846453 0.382788683 -0.023392427 -0.305446080 -0.165393307 -0.374271129 0.09649475 -0.13426507 0.477871640 -0.0621464627 -0.138043968 -0.030890202 0.018796230
gs22 -0.237412025 0.006447096 -0.133865502 0.092070223 0.3746959238 0.17166986 -0.20739838 -0.18006241 -0.09761431 0.068458890 0.101833580 0.20736905 -0.194239535 -0.15737467 0.3344891359 0.190461406 -0.02203098 0.01359537 -0.096586415 0.142655186 -0.099266615 -0.131308533 -0.217519398 -0.32815831 -0.18091395 0.187266495 -0.1299962008 -0.144607465 0.283242500 0.176010459
gs23 0.190415312 0.077045218 0.122323140 0.225229531 0.0556437464 -0.08775647 -0.16727916 0.11798887 -0.01640574 -0.325178292 -0.028746497 -0.25266300 0.220087684 0.12866805 0.2386309465 -0.006614818 -0.30618281 -0.06980429 -0.063318773 0.158561562 -0.156266247 0.030558285 0.217438213 -0.16296449 0.01826912 0.183386259 0.0006773755 -0.050222694 0.011216649 -0.175566800
gs24 0.281822947 -0.250097132 0.276328378 -0.029504134 0.1705584222 -0.33107919 -0.28475345 0.20772600 0.23970926 -0.173997125 -0.441664514 0.10765028 0.195604602 -0.26390827 0.0056296087 0.303057626 0.23985623 -0.23495701 0.465436703 0.096252597 0.054463039 -0.069266265 -0.140740502 -0.13513410 -0.30892914 -0.141877998 0.0032713565 0.248883512 0.473396607 -0.585334293
gs25 0.199849556 0.141623686 0.025047784 -0.110660348 0.2828871008 -0.16169462 -0.28000309 0.23087492 0.37226210 0.187384149 -0.103480250 0.08546276 -0.072181686 -0.02832541 -0.2666116623 0.135112853 -0.12080019 0.30450320 -0.177333096 0.009902668 0.362160182 -0.234464127 -0.053308631 0.01445325 -0.20487586 -0.070595577 -0.2188882525 -0.334186099 0.133468658 -0.029316084
>
> c2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> firPar <- gsvaParam(geneExpCostaEtAl2021, c2BroadSets,
+ minSize=10, maxSize=500)
ℹ No assay name provided; using default assay 'logCPM'
> fir_es <- gsva(firPar, verbose=FALSE)
> assay(fir_es)[seq.int(min(nRowsToPrint, nrow(fir_es))),]
BS03 BS04 BS05 BS06 BS07 BS08 BS09 BS10 BS11 BS12 BS13 BS14 BS16 BS17 BS18 BS19 BS20 BS21 BS22 BS23 BS24
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP 0.02292349 0.12790635 -0.179968777 -0.53107430 -0.659537438 0.45203899 -0.61015343 -0.1413142628 -0.117777932 -0.596835693 0.615435856 0.274946146 -0.41524421 0.39705826 0.35202338 0.050135781 0.257858640 -0.11515971 0.403840241 0.173064103 0.107755544
WINTER_HYPOXIA_UP -0.23987162 -0.12604006 -0.264481894 -0.34346399 -0.397820755 0.23863858 -0.37508089 -0.1335252981 -0.140217740 -0.331601104 0.376283515 0.150845377 0.13023159 0.40599546 0.11528435 -0.009480635 0.053639096 -0.04637949 0.129361851 0.280773073 0.124585543
PARENT_MTOR_SIGNALING_UP -0.01023211 -0.06240698 -0.030713760 0.02678851 0.080531564 0.05423200 0.20395415 0.0271645985 -0.074859366 -0.121317727 -0.099664851 -0.015265185 0.24736481 -0.05285336 -0.16909890 0.070570578 -0.142717585 0.05791113 -0.061313455 -0.024164966 0.014347801
PYEON_HPV_POSITIVE_TUMORS_UP 0.42809640 0.32919003 0.389812309 -0.23278421 -0.209862906 0.09824133 -0.03337240 -0.0607003970 -0.087846994 0.235249450 0.483921506 0.490407343 -0.45257194 -0.38786274 0.15933512 -0.388410321 -0.079215650 -0.22919078 0.115369167 -0.320680827 -0.214079223
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP -0.22750351 -0.22105325 -0.220566467 -0.23490878 -0.364982300 0.12748621 -0.31660045 -0.2139208866 -0.077340363 -0.280979075 0.340735303 -0.087198822 -0.18556247 0.28045230 0.23061930 0.065292446 0.344365500 -0.05134999 0.290138193 0.177470287 0.191859158
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP -0.04740536 0.13150260 -0.302637019 -0.43573567 -0.318388023 -0.29419293 -0.48476141 -0.1708234516 -0.182700833 0.194991420 0.096775852 0.237990325 0.22775317 0.36197706 0.30931300 0.231695063 0.427179760 -0.27098592 -0.083034580 0.368102049 -0.005283552
LU_TUMOR_VASCULATURE_UP 0.22404058 -0.43068932 -0.380600990 0.00236026 0.403950738 -0.09003451 -0.01835083 0.3843713085 -0.034318792 -0.116724831 -0.118200373 -0.181063134 0.37337536 0.00870954 -0.14415171 0.204612942 0.047958533 0.25389697 -0.260712417 0.268384677 -0.267685714
KORKOLA_EMBRYONAL_CARCINOMA_UP -0.04757007 -0.13586445 -0.015447279 -0.50293007 -0.317759661 0.32009785 -0.21377110 -0.2204992126 -0.300076046 -0.138708479 0.420072650 0.124466541 -0.39289128 0.12430012 0.27351406 -0.050506340 0.009461887 0.15557721 -0.079901700 0.327628019 -0.107037370
KORKOLA_TERATOMA_UP 0.46808925 -0.21774496 -0.129682230 -0.39264679 -0.167144223 0.28184319 -0.05816003 -0.2609695799 -0.407058033 0.198844987 0.380908468 -0.090724169 -0.16662244 0.20265846 -0.05412133 0.165060786 -0.061931872 0.35737410 -0.455072189 0.381135317 -0.359773912
KORKOLA_YOLK_SAC_TUMOR_UP -0.16725651 -0.32974789 -0.221800018 -0.48932131 -0.291849820 0.46380803 0.14096780 -0.3865711938 -0.246921657 0.029436052 0.507668708 -0.390282917 -0.51252806 0.21846725 0.37842724 0.023720864 -0.092246760 0.15931049 0.095770965 0.104958264 -0.005095761
KORKOLA_SEMINOMA_UP -0.33562601 -0.28577523 -0.244262534 -0.27800506 -0.069626946 0.32309291 0.08800900 0.0833321577 -0.277191117 -0.099837165 0.282453492 -0.070222343 -0.17513989 -0.01922153 0.05170892 0.329496921 0.138561508 0.14092981 -0.002493429 0.053117518 0.053180172
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP -0.13542260 0.01515806 -0.123710830 -0.15957938 -0.237492560 0.14501130 -0.13338964 0.0572202135 -0.157555272 -0.199427137 0.171315517 0.037788294 0.02258918 0.17076255 0.04897513 0.047182015 -0.054374996 0.23834963 0.018756689 0.256962429 -0.162120270
HOLLMAN_APOPTOSIS_VIA_CD40_UP -0.24952223 -0.22839170 -0.092161117 -0.16513503 -0.228507521 0.15712578 -0.15105318 -0.0007263272 -0.071743015 -0.176708052 0.200717794 -0.060398110 -0.05507417 0.19556884 0.04617003 0.065839300 0.104399289 0.18240655 0.140670149 0.128078917 0.072507958
LIU_PROSTATE_CANCER_UP -0.02530084 -0.28474420 -0.090962845 -0.15503327 -0.148791565 0.24033366 -0.17933889 -0.1445612875 -0.075385781 -0.196033206 0.363058430 0.008430018 -0.08565603 0.08754343 0.11658537 0.027572962 0.093348848 0.08589327 -0.015661941 0.244827565 0.073507178
LIU_SOX4_TARGETS_UP -0.02406433 0.24699598 -0.065885979 0.10154221 -0.122249335 -0.20916134 -0.23055224 -0.0055330354 0.085508371 -0.004532314 -0.150064113 0.122063045 0.00522460 0.22865147 0.15258960 -0.103717219 -0.036804333 0.05202579 0.071969725 0.151502703 -0.145178758
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP 0.21180934 -0.19546723 -0.140082389 -0.10193701 0.005650170 0.05533713 0.06078443 0.0426432072 -0.099630101 -0.006233165 0.128078265 -0.113720741 0.07796755 0.01267864 -0.18849408 0.062068424 0.016825415 0.27151993 -0.176554394 -0.006482359 0.089569220
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP 0.04441846 0.04225478 -0.049898714 -0.13711594 -0.153592793 -0.17120482 -0.40242051 -0.1516006879 -0.170686927 0.229186494 0.032611169 -0.005103335 0.09769941 0.17096206 -0.01281463 0.119646164 0.102260739 0.38260617 -0.238841425 0.449488946 -0.255687685
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP 0.03397928 0.26388388 -0.149410712 -0.07859140 -0.030056165 0.15984260 -0.29834511 -0.3965700456 -0.007409288 -0.174955851 -0.251999452 0.204988714 0.28453515 0.16738681 -0.31311697 0.057903628 0.342199929 0.09401193 -0.006800004 0.092405646 0.134506484
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP -0.38903958 0.09828991 -0.480559229 -0.02241349 -0.155143936 -0.18714452 -0.23277902 0.4840944659 0.365750762 -0.262768901 -0.038041538 0.103290348 -0.28739201 0.24463994 0.12835134 -0.080852874 0.529116082 -0.07419423 0.394703348 0.041489187 -0.279303399
FRASOR_TAMOXIFEN_RESPONSE_UP 0.14513114 0.15204657 -0.011415712 -0.14533939 -0.296185434 -0.03339132 -0.33196505 -0.1347801852 -0.036920881 -0.111410908 -0.075543628 0.046701957 0.11832610 0.15195156 0.10809965 0.055569196 0.071835914 -0.03388644 -0.160697129 0.275314435 0.048533481
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP -0.10766234 0.10322353 -0.364555555 -0.20645899 -0.133541971 0.15573889 -0.21396304 0.0823708144 0.149528954 -0.155237285 -0.007705041 -0.073301722 0.09498367 0.32378661 -0.02198234 0.057138199 0.168222170 0.30591282 0.223683621 -0.063846188 0.109598038
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP 0.27300138 0.17981803 0.005834971 -0.24065397 -0.340627902 -0.07546027 -0.43834122 -0.1917360016 -0.107776808 -0.004744111 0.533808784 0.322443880 -0.45339943 0.08311550 0.34894313 -0.290307573 0.226423203 -0.10026909 0.221255312 0.087976539 -0.259110467
WATANABE_COLON_CANCER_MSI_VS_MSS_UP -0.23657152 -0.18782190 -0.202949000 -0.10513732 -0.497364703 0.36191883 -0.31434211 -0.3891569547 -0.157297886 -0.198849151 0.207380882 0.096259751 0.34514754 -0.23287182 -0.14113604 0.445560091 0.132126827 0.12035394 0.013237341 0.372451838 0.163745844
SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP -0.01857651 0.07156252 -0.204191789 -0.50730032 -0.644390471 0.32055729 -0.56545714 -0.1680683425 -0.273429620 -0.567300383 0.699361412 0.257003106 -0.44168856 0.45577155 0.45041005 -0.269262765 0.250781213 -0.26171756 0.423480829 0.208491300 0.143314032
GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP 0.28776244 0.10484331 0.178368564 -0.05438607 -0.009966795 -0.18753144 -0.17375153 -0.0518374295 0.053535460 0.177138430 0.169801163 0.275453927 -0.15911745 0.06588420 -0.11696977 -0.099197460 -0.157043255 0.27529871 -0.387602857 0.181974900 -0.241074464
>
GSVA.Rcheck/tests/test_plage_newapi.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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>
> ## 2025-11-12 regression test script for method PLAGE
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(geneprotExpCostaEtAl2021)
>
> set.seed(2025-11-12)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 -0.1065910 0.076987224 -1.3963246 1.2771019 -0.3372823
g2 1.6144451 0.006987175 1.2139285 0.9773345 0.2874821
g3 1.3882628 -0.690659025 -2.0385616 0.2804193 -0.1822753
g4 0.7027778 0.562919910 -0.1736422 0.3117396 0.3527060
g5 2.2575002 0.199992976 -0.4118118 0.1876944 0.2664025
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> plagePar <- plageParam(X, gs)
> plage.es <- gsva(plagePar, verbose=FALSE)
> dim(plage.es)
[1] 100 30
> plage.es[seq.int(min(nRowsToPrint, nrow(plage.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 0.167098612 -0.402676200 0.121971573 0.18210410 -0.10002663 -0.271010487 -0.10611360 0.57048850 -0.071107400 0.092018802 0.123999530 0.0606707045 0.13270985 -0.03056144 -0.100718769 -1.446521e-01 0.13846488 -0.095059549 0.13239622 -0.0005756261 -0.001023179 0.034734152 0.10659591 -0.02395647 0.05761513 0.01641592 -0.1948958003 -0.01692843 -0.3979760077 0.019997818
gs2 0.211371181 0.263499028 0.179996853 -0.13111127 -0.24860139 -0.037015393 -0.14527516 0.04215535 0.082501495 0.113369331 -0.007114667 0.0271041386 -0.26346008 -0.17890923 -0.014961197 5.421409e-01 0.14483148 -0.128825166 0.17809010 0.0105117368 -0.060854698 -0.127374903 -0.09240630 0.03622505 -0.19510723 -0.13652509 0.0340764023 -0.36542371 0.1967671136 0.070325368
gs3 -0.026564020 0.433055749 0.039659058 0.15645993 -0.04187768 -0.079826724 -0.27257873 0.07825852 0.365399280 -0.004100745 -0.058264743 0.0478451151 0.10402087 -0.12739196 -0.220032387 4.800603e-02 0.10770770 -0.151163043 -0.03181249 -0.0299662596 0.029370701 -0.005025812 -0.07280132 0.23200909 -0.07831719 -0.40520601 0.2813288972 -0.23104518 -0.2399679208 0.152821294
gs4 -0.056760299 0.290316872 0.324396877 0.03047618 -0.06405277 -0.265214682 0.04728685 0.07335911 0.251218161 0.155898593 -0.098062878 0.0009965108 0.15647866 -0.01541473 -0.331564748 2.148047e-01 0.13290503 0.025202754 -0.04393046 0.2677533214 -0.162268362 0.065118811 -0.16516837 -0.15731406 0.01637255 0.04947816 -0.4723366811 -0.19392104 0.0149132262 -0.090967339
gs5 -0.140013021 0.082660740 0.173871313 -0.15055458 -0.05143034 0.262694549 0.14386015 0.27798280 0.069474244 -0.353611823 -0.070168641 -0.3271325933 -0.24651905 0.23911084 0.083152508 2.735549e-02 -0.26820778 0.233021464 -0.21111034 0.0746902559 -0.012757831 -0.306909613 0.19480764 0.07565827 0.17813359 0.02718080 -0.0552535179 0.15508901 -0.0979187218 -0.007155802
gs6 -0.012226968 -0.025593717 -0.106810081 0.01373246 -0.02808405 0.004490924 0.06681489 -0.31733766 0.014919251 0.028539262 -0.007131531 0.5617619758 0.08745729 -0.03288706 0.349217959 -3.096547e-01 -0.15866230 0.023374475 0.09135112 -0.1745081844 -0.070264384 -0.185726653 0.23285102 0.02873118 0.05176751 -0.18090891 0.3378425065 -0.13994048 -0.0681202238 -0.074994900
gs7 -0.302515729 0.333475000 -0.047067432 0.05192260 0.01849040 -0.051835846 -0.09471292 -0.24690530 -0.170349889 0.177554481 0.269740619 -0.2408773340 -0.20426947 0.10467529 0.161266997 -3.833431e-02 -0.25998880 0.244723491 -0.26099226 0.0670556779 -0.057684643 0.126676391 0.17977070 0.30431749 0.21640391 0.03771753 -0.0039912225 -0.21036552 0.0009697554 -0.104869665
gs8 0.219782456 0.183673388 -0.212202405 -0.04237083 -0.08661547 -0.245755451 0.35298091 0.12649187 0.080060210 0.164890093 0.051848550 0.0530899306 -0.27228490 0.09926297 -0.060723550 3.675507e-01 0.18311519 -0.249584630 0.15097149 0.1816526869 0.020305566 -0.164245134 -0.27179969 -0.06778968 -0.18186429 -0.26487815 0.1134764862 -0.03151877 -0.0409791425 -0.156540432
gs9 -0.082547644 0.171986233 0.099496364 0.22572686 0.26488943 0.013666173 -0.08205537 0.16132217 0.017484676 -0.069740219 0.105548659 0.0032195026 0.47119886 -0.05654433 -0.358350549 -2.275253e-01 0.02488244 0.026703883 -0.22558894 -0.1497645265 -0.343297306 -0.135483489 -0.06033080 -0.14344239 0.28754792 0.12834087 -0.1488742506 0.14055401 -0.0328441969 -0.026178760
gs10 -0.007073239 -0.234054734 0.235931932 -0.22203099 -0.01167826 0.064110426 -0.13039724 0.27572995 -0.123129046 -0.186990096 0.074445699 0.0562089221 -0.18050428 0.46242539 -0.080101878 -2.906945e-01 0.19599682 0.279404588 0.27021869 0.0010602531 -0.060403819 -0.006513772 -0.22773798 -0.19604378 -0.01351890 0.15909823 0.0098724163 0.08939823 -0.0341395185 -0.168889512
gs11 -0.169578001 0.146897757 -0.234382621 -0.01500993 -0.23785840 0.049334252 0.11279024 0.01862949 -0.110828893 0.029622040 -0.041525421 -0.2218623033 0.01589633 0.15321638 0.332005755 1.634773e-01 -0.19161877 -0.251207204 0.07976858 0.1671691441 -0.014071471 -0.112945473 -0.01938753 0.36081217 0.24963503 -0.17869516 -0.1930416245 0.11128119 0.2974621023 -0.295984939
gs12 0.112495756 -0.138770944 0.001976133 0.02843095 0.10580500 0.174981373 -0.10510562 -0.23971400 -0.024758670 -0.068276471 -0.053683183 -0.3525460231 0.28667349 0.05948858 -0.137808031 4.822800e-02 -0.08708531 -0.113239358 0.26197642 0.2527964679 0.075818410 0.210243693 -0.10467131 0.34078111 0.15790923 -0.03015219 0.0840320017 -0.24827228 -0.4347351144 -0.062818106
gs13 0.377575452 -0.211317696 0.075273081 0.08664049 0.35519123 -0.121575218 0.27433434 0.04442173 -0.009410830 0.029131700 0.175283796 -0.1498012831 -0.19074531 -0.20093311 -0.122340694 -1.719853e-01 0.09547356 -0.124071968 -0.11493657 -0.2493740603 -0.124605424 0.047955845 0.04410248 0.33165636 0.20026632 0.05908495 -0.1803721877 -0.07872341 0.1310315453 -0.277229850
gs14 0.119882841 0.066275089 0.051617722 0.63436623 -0.18489675 0.061455008 -0.06433563 -0.16770797 0.001935058 0.015168754 0.021499965 -0.0966592523 -0.18568394 -0.05348614 -0.322192065 -9.815223e-02 -0.08404944 -0.056553147 -0.04718185 -0.1200311343 0.399345875 0.088933524 -0.05118790 0.09095227 -0.08650982 -0.24798818 0.0993975382 0.20336404 0.1052846126 -0.092863079
gs15 -0.174611492 -0.156492994 -0.161021319 -0.04699889 -0.18505192 0.232787907 0.30431059 -0.18744808 0.193023682 -0.177828459 0.074812816 0.2533367081 -0.09950995 -0.15400881 -0.113210676 3.790107e-01 -0.01474583 0.231430867 0.14027506 -0.1578394130 -0.167030214 -0.105705770 0.08194637 -0.10462642 -0.36534861 0.01680513 0.0072505236 0.21012097 0.0578118649 0.188555656
gs16 0.049228105 0.390411888 -0.060006352 0.01564146 0.13261456 0.213856387 0.03713845 -0.15392163 0.192611856 -0.175272848 0.269224795 -0.0567265976 -0.12078233 0.23397180 -0.207932895 1.268676e-01 -0.12993599 0.001792767 0.13273758 0.1617978542 -0.194663678 -0.033707472 0.25018937 -0.22850878 0.07423389 -0.42808303 -0.0936582936 -0.21726999 -0.1405788159 -0.041269678
gs17 -0.122472919 -0.213976638 -0.151621286 0.10282553 0.31286659 0.120335818 0.12341332 0.20974328 -0.142459036 0.094989852 0.346058602 0.0501723070 -0.23245151 0.01477261 0.253589555 -1.548802e-01 -0.09428269 -0.082192169 -0.09863229 -0.1123492121 -0.254476726 0.136455830 -0.04711922 0.11521623 0.04934160 -0.39702227 -0.2667835923 0.20631663 0.0879006652 0.146721324
gs18 0.171306063 -0.328873464 0.236471950 -0.08219078 -0.13237682 0.162439130 0.06430284 0.17784211 0.132115265 0.246786971 0.270256729 -0.1401882091 0.21455327 -0.17165724 -0.249813484 -1.352758e-01 0.31271153 -0.215107365 0.08121373 -0.2531840114 -0.035444886 0.222955099 -0.09562192 -0.20814785 0.14960783 -0.06159646 -0.1213719857 0.03732329 -0.0981355707 -0.150899981
gs19 0.012637849 -0.060144725 -0.005960217 -0.18519337 -0.02020765 0.059756159 0.25796421 -0.20698563 0.112698963 0.333337981 -0.317786962 -0.2887281774 0.28956267 0.11584899 -0.303698509 -1.746562e-01 -0.27059001 -0.041237088 0.06360957 0.0528160839 0.153743785 0.076128094 -0.01399102 0.13530741 0.18607255 0.15362658 -0.1146532793 -0.28024485 0.1657884967 0.115178297
gs20 -0.073168773 0.011217875 -0.094703381 -0.09078283 0.19542027 -0.264701277 -0.20288283 -0.00399427 -0.002442221 -0.127676098 0.374715081 0.2461288340 -0.11847511 0.16442120 0.210561003 1.108443e-01 -0.13417209 -0.009681263 -0.07186602 -0.1706995132 -0.320764880 0.001134938 0.09476864 -0.09017845 0.07033344 -0.15824836 0.3865012420 0.33996612 -0.0699993164 -0.201576249
gs21 0.325374654 -0.139691833 -0.186027791 0.16721234 -0.02832459 0.315904252 0.06200808 0.07652501 -0.020171638 -0.343892261 0.352515322 0.1837208332 -0.02370014 -0.21446002 -0.213068376 8.636064e-05 0.13391681 0.162748451 -0.32239861 0.1670229926 -0.123912296 0.033247132 0.03656189 -0.11239260 0.09382195 -0.28946322 -0.1539560727 -0.04446368 0.0887734497 0.016483597
gs22 0.055121457 -0.166608114 -0.146812748 0.15152002 0.53962484 0.123319797 0.24415985 0.06154368 0.007360281 -0.190853762 0.079497835 0.1334235072 -0.01096890 -0.05281625 -0.170578785 -7.370118e-02 -0.13105726 -0.075362692 -0.04185400 -0.1236638627 0.040695814 -0.116436911 -0.07505105 0.06543913 -0.08266636 -0.27051298 0.2301327540 0.41442528 -0.2118152101 -0.205504188
gs23 -0.024216292 0.004152364 -0.164896887 -0.33501455 -0.15822163 -0.001509253 0.08354573 -0.01441183 0.099937608 0.187568474 -0.063189957 0.4850722043 -0.07024477 0.35911691 -0.498719667 1.389035e-01 0.14910589 -0.062139744 -0.19577814 -0.1033935648 0.020675007 -0.142054640 0.05822014 -0.03654423 0.01144530 0.07758937 -0.0158634656 0.17591413 -0.0210582545 0.056010221
gs24 -0.146570337 0.366073340 -0.138397761 -0.11782833 0.06565496 0.068330247 0.06040254 -0.04783993 -0.343210952 0.058750971 0.012662925 0.3041965302 0.05850315 0.17599583 -0.008434218 -1.054991e-01 -0.32170281 0.160599608 -0.38523110 -0.1262752757 -0.214033397 0.046923250 0.06444254 0.07806126 0.15436592 0.26527217 0.0002913013 -0.01596741 -0.1971408858 0.227604954
gs25 -0.162135128 0.230952812 0.292823140 -0.15002469 0.12515411 0.132286866 -0.29589045 0.04908425 -0.080454383 0.157068355 0.093252860 -0.2725953637 0.14092402 -0.16859763 -0.206489759 -2.283688e-01 -0.16073197 -0.216276395 -0.28487183 0.2588007263 0.261534289 -0.087390434 0.11880495 0.13537426 0.16208594 0.13673304 0.0902327045 -0.18476075 -0.0098617691 0.123337039
>
> c2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> firPar <- plageParam(geneExpCostaEtAl2021, c2BroadSets,
+ minSize=10, maxSize=500)
ℹ No assay name provided; using default assay 'logCPM'
> fir_es <- gsva(firPar, verbose=FALSE)
> assay(fir_es)[seq.int(min(nRowsToPrint, nrow(fir_es))),]
BS03 BS04 BS05 BS06 BS07 BS08 BS09 BS10 BS11 BS12 BS13 BS14 BS16 BS17 BS18 BS19 BS20 BS21 BS22 BS23 BS24
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP 0.019078855 0.0447322833 0.081037806 -0.12573681 -0.302466753 0.124794815 -0.443323310 -0.02821304 -0.05921282 -0.2091788861 0.66869123 0.17660131 -0.21309254 0.148592621 0.14101158 -0.138348238 -0.02132215 -0.06048096 0.11634013 0.13476931 -0.054274434
WINTER_HYPOXIA_UP 0.185132391 0.0605863802 0.186881343 0.20184358 0.304379522 -0.027095512 0.330636528 0.13842903 0.07265825 0.1309538102 -0.56712562 -0.06712794 0.14693498 -0.384037963 -0.15496630 0.018763553 -0.13149256 0.01203135 -0.27036577 -0.17864904 -0.008370025
PARENT_MTOR_SIGNALING_UP 0.033600601 -0.0977636532 -0.010379401 0.16490218 0.160091329 0.034072029 0.546848316 0.12358665 0.08545840 -0.0202792379 -0.35142424 -0.17920950 0.16889699 -0.400726655 -0.22629235 0.190079477 -0.02601476 -0.01699046 -0.16947006 -0.27963289 0.270647230
PYEON_HPV_POSITIVE_TUMORS_UP -0.105585157 -0.0246063960 -0.185692228 0.13219011 0.236620501 -0.081066426 0.119501531 0.11788789 0.11697213 0.0370405224 -0.69686154 -0.41377128 0.30280567 0.116275645 -0.06028385 0.192238764 0.02741594 0.13377829 -0.01125434 -0.04013456 0.086528783
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP -0.140949992 -0.0320884452 -0.141281108 -0.12634839 -0.256560903 -0.018929107 -0.376890461 -0.08773797 -0.03981076 -0.1200607404 0.59295342 0.01732524 -0.23687578 0.275629919 0.21997200 -0.088174492 0.13998839 -0.02102343 0.35360586 0.14906191 -0.061805178
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP 0.154002684 0.0471026944 0.178371760 -0.18641893 -0.124311182 -0.023579568 -0.331625977 -0.05693586 -0.14012857 0.0731375473 0.45314684 0.30977009 -0.03984580 0.321918969 -0.04098719 -0.157534791 -0.09110255 0.04006637 -0.37214249 0.28662614 -0.299530188
LU_TUMOR_VASCULATURE_UP 0.289063026 0.1921571735 0.291438706 0.02898286 0.028563016 0.427070743 0.158380330 -0.11433305 -0.01452374 -0.0190169998 -0.19593804 0.26400076 -0.02450408 -0.051094542 -0.13289925 -0.217746171 -0.40403077 0.12149266 -0.44698830 -0.06339733 -0.116677000
KORKOLA_EMBRYONAL_CARCINOMA_UP -0.012381621 -0.0083399791 0.041673582 0.27151117 0.274276674 -0.118455758 0.407022036 0.19753310 0.12611837 -0.0026633778 -0.38004554 -0.24376771 0.16849466 -0.492826322 0.01324333 -0.014598000 -0.09191430 0.01553458 0.01912555 -0.32510552 0.155565067
KORKOLA_TERATOMA_UP -0.066550845 -0.0778349779 -0.061092636 -0.26462646 -0.278265851 0.180696377 -0.415139463 -0.18838941 -0.10282333 0.0007663447 0.41973253 0.09122991 -0.19128560 0.453557804 0.03219706 0.052482498 0.08282759 0.06631649 0.08371914 0.33797427 -0.155491437
KORKOLA_YOLK_SAC_TUMOR_UP 0.159150582 0.0692505640 0.241977555 0.26105264 0.323258336 -0.153376938 0.236590304 0.09118202 0.14258869 0.0091716057 -0.56593676 0.02260408 0.23449933 -0.366843770 -0.08226032 -0.136739634 -0.05149173 0.01409559 -0.18549824 -0.23819262 -0.025081298
KORKOLA_SEMINOMA_UP -0.010803841 0.0223122457 -0.003183776 -0.28018868 -0.265518330 0.016333121 -0.437892513 -0.16424287 -0.09310584 -0.0031009245 0.38328333 0.19685357 -0.19826157 0.456438358 0.09924863 -0.042311302 0.11555842 0.05177458 0.10394153 0.29985730 -0.246991431
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP 0.300224203 0.0962617246 0.414419345 0.04944886 0.117404841 0.075958938 0.224771230 -0.05156950 -0.02527373 0.0852667630 -0.20311700 0.24544874 0.10691293 -0.284444595 -0.27620982 -0.009992413 -0.15805341 -0.04069048 -0.58777097 -0.02720379 -0.051791865
HOLLMAN_APOPTOSIS_VIA_CD40_UP 0.159694118 0.0410536329 0.308668575 -0.12645484 -0.135319598 0.081107747 -0.319683205 -0.15899857 -0.16425438 0.0416693122 0.39281210 0.37753381 -0.13823891 0.167054476 -0.09557144 -0.123686107 -0.08994822 0.05111214 -0.33152469 0.33937060 -0.276396548
LIU_PROSTATE_CANCER_UP -0.200174601 -0.1024275640 -0.362769398 0.09620792 0.099175486 -0.064794023 0.327178382 0.18176145 0.14724468 -0.0478676575 -0.19636413 -0.37273481 0.06123468 -0.211530468 0.12140292 0.145476074 0.12739982 -0.13649384 0.35560281 -0.30529388 0.337766146
LIU_SOX4_TARGETS_UP -0.311115716 -0.0150999573 -0.370183270 0.02994648 0.007097133 -0.143160600 0.033179407 0.07347206 0.18075497 -0.0490631058 -0.13686508 -0.32569959 -0.04179661 0.071504493 0.25096389 0.077471847 0.21601436 -0.10244245 0.56524112 -0.25566844 0.245449068
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP -0.003982591 -0.0048376318 -0.110590132 0.20962500 0.165784093 0.006158587 0.461154480 0.14141161 0.13438601 0.0139659018 -0.51453201 -0.21847873 0.16418941 -0.369435533 -0.08635541 0.116735516 -0.02053522 0.03207892 -0.02647942 -0.32984473 0.239581866
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP 0.196501118 0.1026796537 0.240480585 -0.18619747 -0.078668907 0.006782133 -0.396278177 -0.06026344 -0.13359799 0.0137103217 0.25372378 0.31124485 0.02798112 0.261278988 -0.08560173 -0.168912257 -0.14454218 0.15143993 -0.35932984 0.36523086 -0.317661358
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP 0.195155486 0.0436878545 0.283825023 -0.19057341 -0.128414352 0.126639281 -0.230096834 -0.11125278 -0.16040060 0.0141769764 0.33836970 0.39001187 -0.06716428 0.242054659 -0.11258298 -0.266989610 -0.20349225 0.11360442 -0.30398607 0.29530770 -0.267879809
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP -0.294986347 0.0052927646 -0.356404299 0.11700956 -0.007887195 -0.086973052 -0.119261750 0.11415343 0.18703738 -0.0850102920 -0.05905421 -0.22051299 -0.13333692 0.063606967 0.29966264 -0.048516693 0.20245527 -0.07809657 0.67318459 -0.16966935 -0.002692925
FRASOR_TAMOXIFEN_RESPONSE_UP 0.188023524 0.0671210477 0.343491341 -0.07224244 0.049987182 0.005442805 -0.302414575 -0.05126835 -0.11773410 -0.0005034533 0.35344430 0.32597292 0.01419023 0.117754298 -0.16043707 -0.220436563 -0.20630553 0.12176178 -0.41686194 0.27627834 -0.315263740
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP 0.241880857 0.0105397235 0.347036800 -0.05973739 -0.062325297 0.069763158 -0.244608962 -0.06881315 -0.15614365 0.0243455638 0.35066650 0.32051680 -0.08383109 0.163672422 -0.15691721 -0.160817100 -0.21680375 0.08005991 -0.37514696 0.31594804 -0.339285197
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP -0.047998545 -0.0323723167 -0.060572908 0.16022173 0.275719671 -0.057408832 0.361535917 0.10716517 0.09414650 0.1002458630 -0.70393793 -0.26211976 0.25219492 -0.157844533 -0.09582946 0.126761665 -0.02440087 0.04045981 -0.07101498 -0.14668627 0.141735147
WATANABE_COLON_CANCER_MSI_VS_MSS_UP 0.201880848 0.0196443300 0.365010142 -0.11550445 -0.138797871 0.055947801 -0.007487674 -0.08694755 -0.14910284 0.0015427813 0.05838620 0.34951692 0.23248606 -0.088092361 -0.22754227 0.010672324 -0.19455170 0.13708637 -0.54111765 0.34525759 -0.228287022
SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP 0.013311652 -0.0003007427 0.023933970 0.16533251 0.319064898 -0.095372252 0.334778888 0.07494605 0.08931846 0.1961254232 -0.72402030 -0.14988899 0.22108366 -0.172773667 -0.14558504 0.074353483 -0.02784261 0.06165634 -0.17637553 -0.09439616 0.012649956
GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP -0.232713928 -0.1231571531 -0.436437041 0.03317630 0.055894544 0.009764435 0.173788487 0.07191884 0.11197173 -0.0962980513 -0.11688596 -0.28262921 -0.07519009 -0.009788198 0.31897933 0.099158027 0.14456325 -0.10034534 0.55453314 -0.29946776 0.199164634
>
> proc.time()
user system elapsed
6.136 0.222 6.721
GSVA.Rcheck/tests/test_plage_newapi.Rout.save
R Under development (unstable) (2025-10-28 r88976) -- "Unsuffered Consequences"
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>
> ## 2025-11-12 regression test script for method PLAGE
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(geneprotExpCostaEtAl2021)
>
> set.seed(2025-11-12)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 -0.1065910 0.076987224 -1.3963246 1.2771019 -0.3372823
g2 1.6144451 0.006987175 1.2139285 0.9773345 0.2874821
g3 1.3882628 -0.690659025 -2.0385616 0.2804193 -0.1822753
g4 0.7027778 0.562919910 -0.1736422 0.3117396 0.3527060
g5 2.2575002 0.199992976 -0.4118118 0.1876944 0.2664025
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> plagePar <- plageParam(X, gs)
> plage.es <- gsva(plagePar, verbose=FALSE)
> dim(plage.es)
[1] 100 30
> plage.es[seq.int(min(nRowsToPrint, nrow(plage.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 0.167098612 -0.402676200 0.121971573 0.18210410 -0.10002663 -0.271010487 -0.10611360 0.57048850 -0.071107400 0.092018802 0.123999530 0.0606707045 0.13270985 -0.03056144 -0.100718769 -1.446521e-01 0.13846488 -0.095059549 0.13239622 -0.0005756261 -0.001023179 0.034734152 0.10659591 -0.02395647 0.05761513 0.01641592 -0.1948958003 -0.01692843 -0.3979760077 0.019997818
gs2 0.211371181 0.263499028 0.179996853 -0.13111127 -0.24860139 -0.037015393 -0.14527516 0.04215535 0.082501495 0.113369331 -0.007114667 0.0271041386 -0.26346008 -0.17890923 -0.014961197 5.421409e-01 0.14483148 -0.128825166 0.17809010 0.0105117368 -0.060854698 -0.127374903 -0.09240630 0.03622505 -0.19510723 -0.13652509 0.0340764023 -0.36542371 0.1967671136 0.070325368
gs3 -0.026564020 0.433055749 0.039659058 0.15645993 -0.04187768 -0.079826724 -0.27257873 0.07825852 0.365399280 -0.004100745 -0.058264743 0.0478451151 0.10402087 -0.12739196 -0.220032387 4.800603e-02 0.10770770 -0.151163043 -0.03181249 -0.0299662596 0.029370701 -0.005025812 -0.07280132 0.23200909 -0.07831719 -0.40520601 0.2813288972 -0.23104518 -0.2399679208 0.152821294
gs4 -0.056760299 0.290316872 0.324396877 0.03047618 -0.06405277 -0.265214682 0.04728685 0.07335911 0.251218161 0.155898593 -0.098062878 0.0009965108 0.15647866 -0.01541473 -0.331564748 2.148047e-01 0.13290503 0.025202754 -0.04393046 0.2677533214 -0.162268362 0.065118811 -0.16516837 -0.15731406 0.01637255 0.04947816 -0.4723366811 -0.19392104 0.0149132262 -0.090967339
gs5 -0.140013021 0.082660740 0.173871313 -0.15055458 -0.05143034 0.262694549 0.14386015 0.27798280 0.069474244 -0.353611823 -0.070168641 -0.3271325933 -0.24651905 0.23911084 0.083152508 2.735549e-02 -0.26820778 0.233021464 -0.21111034 0.0746902559 -0.012757831 -0.306909613 0.19480764 0.07565827 0.17813359 0.02718080 -0.0552535179 0.15508901 -0.0979187218 -0.007155802
gs6 -0.012226968 -0.025593717 -0.106810081 0.01373246 -0.02808405 0.004490924 0.06681489 -0.31733766 0.014919251 0.028539262 -0.007131531 0.5617619758 0.08745729 -0.03288706 0.349217959 -3.096547e-01 -0.15866230 0.023374475 0.09135112 -0.1745081844 -0.070264384 -0.185726653 0.23285102 0.02873118 0.05176751 -0.18090891 0.3378425065 -0.13994048 -0.0681202238 -0.074994900
gs7 -0.302515729 0.333475000 -0.047067432 0.05192260 0.01849040 -0.051835846 -0.09471292 -0.24690530 -0.170349889 0.177554481 0.269740619 -0.2408773340 -0.20426947 0.10467529 0.161266997 -3.833431e-02 -0.25998880 0.244723491 -0.26099226 0.0670556779 -0.057684643 0.126676391 0.17977070 0.30431749 0.21640391 0.03771753 -0.0039912225 -0.21036552 0.0009697554 -0.104869665
gs8 0.219782456 0.183673388 -0.212202405 -0.04237083 -0.08661547 -0.245755451 0.35298091 0.12649187 0.080060210 0.164890093 0.051848550 0.0530899306 -0.27228490 0.09926297 -0.060723550 3.675507e-01 0.18311519 -0.249584630 0.15097149 0.1816526869 0.020305566 -0.164245134 -0.27179969 -0.06778968 -0.18186429 -0.26487815 0.1134764862 -0.03151877 -0.0409791425 -0.156540432
gs9 -0.082547644 0.171986233 0.099496364 0.22572686 0.26488943 0.013666173 -0.08205537 0.16132217 0.017484676 -0.069740219 0.105548659 0.0032195026 0.47119886 -0.05654433 -0.358350549 -2.275253e-01 0.02488244 0.026703883 -0.22558894 -0.1497645265 -0.343297306 -0.135483489 -0.06033080 -0.14344239 0.28754792 0.12834087 -0.1488742506 0.14055401 -0.0328441969 -0.026178760
gs10 -0.007073239 -0.234054734 0.235931932 -0.22203099 -0.01167826 0.064110426 -0.13039724 0.27572995 -0.123129046 -0.186990096 0.074445699 0.0562089221 -0.18050428 0.46242539 -0.080101878 -2.906945e-01 0.19599682 0.279404588 0.27021869 0.0010602531 -0.060403819 -0.006513772 -0.22773798 -0.19604378 -0.01351890 0.15909823 0.0098724163 0.08939823 -0.0341395185 -0.168889512
gs11 -0.169578001 0.146897757 -0.234382621 -0.01500993 -0.23785840 0.049334252 0.11279024 0.01862949 -0.110828893 0.029622040 -0.041525421 -0.2218623033 0.01589633 0.15321638 0.332005755 1.634773e-01 -0.19161877 -0.251207204 0.07976858 0.1671691441 -0.014071471 -0.112945473 -0.01938753 0.36081217 0.24963503 -0.17869516 -0.1930416245 0.11128119 0.2974621023 -0.295984939
gs12 0.112495756 -0.138770944 0.001976133 0.02843095 0.10580500 0.174981373 -0.10510562 -0.23971400 -0.024758670 -0.068276471 -0.053683183 -0.3525460231 0.28667349 0.05948858 -0.137808031 4.822800e-02 -0.08708531 -0.113239358 0.26197642 0.2527964679 0.075818410 0.210243693 -0.10467131 0.34078111 0.15790923 -0.03015219 0.0840320017 -0.24827228 -0.4347351144 -0.062818106
gs13 0.377575452 -0.211317696 0.075273081 0.08664049 0.35519123 -0.121575218 0.27433434 0.04442173 -0.009410830 0.029131700 0.175283796 -0.1498012831 -0.19074531 -0.20093311 -0.122340694 -1.719853e-01 0.09547356 -0.124071968 -0.11493657 -0.2493740603 -0.124605424 0.047955845 0.04410248 0.33165636 0.20026632 0.05908495 -0.1803721877 -0.07872341 0.1310315453 -0.277229850
gs14 0.119882841 0.066275089 0.051617722 0.63436623 -0.18489675 0.061455008 -0.06433563 -0.16770797 0.001935058 0.015168754 0.021499965 -0.0966592523 -0.18568394 -0.05348614 -0.322192065 -9.815223e-02 -0.08404944 -0.056553147 -0.04718185 -0.1200311343 0.399345875 0.088933524 -0.05118790 0.09095227 -0.08650982 -0.24798818 0.0993975382 0.20336404 0.1052846126 -0.092863079
gs15 -0.174611492 -0.156492994 -0.161021319 -0.04699889 -0.18505192 0.232787907 0.30431059 -0.18744808 0.193023682 -0.177828459 0.074812816 0.2533367081 -0.09950995 -0.15400881 -0.113210676 3.790107e-01 -0.01474583 0.231430867 0.14027506 -0.1578394130 -0.167030214 -0.105705770 0.08194637 -0.10462642 -0.36534861 0.01680513 0.0072505236 0.21012097 0.0578118649 0.188555656
gs16 0.049228105 0.390411888 -0.060006352 0.01564146 0.13261456 0.213856387 0.03713845 -0.15392163 0.192611856 -0.175272848 0.269224795 -0.0567265976 -0.12078233 0.23397180 -0.207932895 1.268676e-01 -0.12993599 0.001792767 0.13273758 0.1617978542 -0.194663678 -0.033707472 0.25018937 -0.22850878 0.07423389 -0.42808303 -0.0936582936 -0.21726999 -0.1405788159 -0.041269678
gs17 -0.122472919 -0.213976638 -0.151621286 0.10282553 0.31286659 0.120335818 0.12341332 0.20974328 -0.142459036 0.094989852 0.346058602 0.0501723070 -0.23245151 0.01477261 0.253589555 -1.548802e-01 -0.09428269 -0.082192169 -0.09863229 -0.1123492121 -0.254476726 0.136455830 -0.04711922 0.11521623 0.04934160 -0.39702227 -0.2667835923 0.20631663 0.0879006652 0.146721324
gs18 0.171306063 -0.328873464 0.236471950 -0.08219078 -0.13237682 0.162439130 0.06430284 0.17784211 0.132115265 0.246786971 0.270256729 -0.1401882091 0.21455327 -0.17165724 -0.249813484 -1.352758e-01 0.31271153 -0.215107365 0.08121373 -0.2531840114 -0.035444886 0.222955099 -0.09562192 -0.20814785 0.14960783 -0.06159646 -0.1213719857 0.03732329 -0.0981355707 -0.150899981
gs19 0.012637849 -0.060144725 -0.005960217 -0.18519337 -0.02020765 0.059756159 0.25796421 -0.20698563 0.112698963 0.333337981 -0.317786962 -0.2887281774 0.28956267 0.11584899 -0.303698509 -1.746562e-01 -0.27059001 -0.041237088 0.06360957 0.0528160839 0.153743785 0.076128094 -0.01399102 0.13530741 0.18607255 0.15362658 -0.1146532793 -0.28024485 0.1657884967 0.115178297
gs20 -0.073168773 0.011217875 -0.094703381 -0.09078283 0.19542027 -0.264701277 -0.20288283 -0.00399427 -0.002442221 -0.127676098 0.374715081 0.2461288340 -0.11847511 0.16442120 0.210561003 1.108443e-01 -0.13417209 -0.009681263 -0.07186602 -0.1706995132 -0.320764880 0.001134938 0.09476864 -0.09017845 0.07033344 -0.15824836 0.3865012420 0.33996612 -0.0699993164 -0.201576249
gs21 0.325374654 -0.139691833 -0.186027791 0.16721234 -0.02832459 0.315904252 0.06200808 0.07652501 -0.020171638 -0.343892261 0.352515322 0.1837208332 -0.02370014 -0.21446002 -0.213068376 8.636064e-05 0.13391681 0.162748451 -0.32239861 0.1670229926 -0.123912296 0.033247132 0.03656189 -0.11239260 0.09382195 -0.28946322 -0.1539560727 -0.04446368 0.0887734497 0.016483597
gs22 0.055121457 -0.166608114 -0.146812748 0.15152002 0.53962484 0.123319797 0.24415985 0.06154368 0.007360281 -0.190853762 0.079497835 0.1334235072 -0.01096890 -0.05281625 -0.170578785 -7.370118e-02 -0.13105726 -0.075362692 -0.04185400 -0.1236638627 0.040695814 -0.116436911 -0.07505105 0.06543913 -0.08266636 -0.27051298 0.2301327540 0.41442528 -0.2118152101 -0.205504188
gs23 -0.024216292 0.004152364 -0.164896887 -0.33501455 -0.15822163 -0.001509253 0.08354573 -0.01441183 0.099937608 0.187568474 -0.063189957 0.4850722043 -0.07024477 0.35911691 -0.498719667 1.389035e-01 0.14910589 -0.062139744 -0.19577814 -0.1033935648 0.020675007 -0.142054640 0.05822014 -0.03654423 0.01144530 0.07758937 -0.0158634656 0.17591413 -0.0210582545 0.056010221
gs24 -0.146570337 0.366073340 -0.138397761 -0.11782833 0.06565496 0.068330247 0.06040254 -0.04783993 -0.343210952 0.058750971 0.012662925 0.3041965302 0.05850315 0.17599583 -0.008434218 -1.054991e-01 -0.32170281 0.160599608 -0.38523110 -0.1262752757 -0.214033397 0.046923250 0.06444254 0.07806126 0.15436592 0.26527217 0.0002913013 -0.01596741 -0.1971408858 0.227604954
gs25 -0.162135128 0.230952812 0.292823140 -0.15002469 0.12515411 0.132286866 -0.29589045 0.04908425 -0.080454383 0.157068355 0.093252860 -0.2725953637 0.14092402 -0.16859763 -0.206489759 -2.283688e-01 -0.16073197 -0.216276395 -0.28487183 0.2588007263 0.261534289 -0.087390434 0.11880495 0.13537426 0.16208594 0.13673304 0.0902327045 -0.18476075 -0.0098617691 0.123337039
>
> c2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> firPar <- plageParam(geneExpCostaEtAl2021, c2BroadSets,
+ minSize=10, maxSize=500)
ℹ No assay name provided; using default assay 'logCPM'
> fir_es <- gsva(firPar, verbose=FALSE)
> assay(fir_es)[seq.int(min(nRowsToPrint, nrow(fir_es))),]
BS03 BS04 BS05 BS06 BS07 BS08 BS09 BS10 BS11 BS12 BS13 BS14 BS16 BS17 BS18 BS19 BS20 BS21 BS22 BS23 BS24
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP 0.019078855 0.0447322833 0.081037806 -0.12573681 -0.302466753 0.124794815 -0.443323310 -0.02821304 -0.05921282 -0.2091788861 0.66869123 0.17660131 -0.21309254 0.148592621 0.14101158 -0.138348238 -0.02132215 -0.06048096 0.11634013 0.13476931 -0.054274434
WINTER_HYPOXIA_UP 0.185132391 0.0605863802 0.186881343 0.20184358 0.304379522 -0.027095512 0.330636528 0.13842903 0.07265825 0.1309538102 -0.56712562 -0.06712794 0.14693498 -0.384037963 -0.15496630 0.018763553 -0.13149256 0.01203135 -0.27036577 -0.17864904 -0.008370025
PARENT_MTOR_SIGNALING_UP 0.033600601 -0.0977636532 -0.010379401 0.16490218 0.160091329 0.034072029 0.546848316 0.12358665 0.08545840 -0.0202792379 -0.35142424 -0.17920950 0.16889699 -0.400726655 -0.22629235 0.190079477 -0.02601476 -0.01699046 -0.16947006 -0.27963289 0.270647230
PYEON_HPV_POSITIVE_TUMORS_UP -0.105585157 -0.0246063960 -0.185692228 0.13219011 0.236620501 -0.081066426 0.119501531 0.11788789 0.11697213 0.0370405224 -0.69686154 -0.41377128 0.30280567 0.116275645 -0.06028385 0.192238764 0.02741594 0.13377829 -0.01125434 -0.04013456 0.086528783
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP -0.140949992 -0.0320884452 -0.141281108 -0.12634839 -0.256560903 -0.018929107 -0.376890461 -0.08773797 -0.03981076 -0.1200607404 0.59295342 0.01732524 -0.23687578 0.275629919 0.21997200 -0.088174492 0.13998839 -0.02102343 0.35360586 0.14906191 -0.061805178
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP 0.154002684 0.0471026944 0.178371760 -0.18641893 -0.124311182 -0.023579568 -0.331625977 -0.05693586 -0.14012857 0.0731375473 0.45314684 0.30977009 -0.03984580 0.321918969 -0.04098719 -0.157534791 -0.09110255 0.04006637 -0.37214249 0.28662614 -0.299530188
LU_TUMOR_VASCULATURE_UP 0.289063026 0.1921571735 0.291438706 0.02898286 0.028563016 0.427070743 0.158380330 -0.11433305 -0.01452374 -0.0190169998 -0.19593804 0.26400076 -0.02450408 -0.051094542 -0.13289925 -0.217746171 -0.40403077 0.12149266 -0.44698830 -0.06339733 -0.116677000
KORKOLA_EMBRYONAL_CARCINOMA_UP -0.012381621 -0.0083399791 0.041673582 0.27151117 0.274276674 -0.118455758 0.407022036 0.19753310 0.12611837 -0.0026633778 -0.38004554 -0.24376771 0.16849466 -0.492826322 0.01324333 -0.014598000 -0.09191430 0.01553458 0.01912555 -0.32510552 0.155565067
KORKOLA_TERATOMA_UP -0.066550845 -0.0778349779 -0.061092636 -0.26462646 -0.278265851 0.180696377 -0.415139463 -0.18838941 -0.10282333 0.0007663447 0.41973253 0.09122991 -0.19128560 0.453557804 0.03219706 0.052482498 0.08282759 0.06631649 0.08371914 0.33797427 -0.155491437
KORKOLA_YOLK_SAC_TUMOR_UP 0.159150582 0.0692505640 0.241977555 0.26105264 0.323258336 -0.153376938 0.236590304 0.09118202 0.14258869 0.0091716057 -0.56593676 0.02260408 0.23449933 -0.366843770 -0.08226032 -0.136739634 -0.05149173 0.01409559 -0.18549824 -0.23819262 -0.025081298
KORKOLA_SEMINOMA_UP -0.010803841 0.0223122457 -0.003183776 -0.28018868 -0.265518330 0.016333121 -0.437892513 -0.16424287 -0.09310584 -0.0031009245 0.38328333 0.19685357 -0.19826157 0.456438358 0.09924863 -0.042311302 0.11555842 0.05177458 0.10394153 0.29985730 -0.246991431
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP 0.300224203 0.0962617246 0.414419345 0.04944886 0.117404841 0.075958938 0.224771230 -0.05156950 -0.02527373 0.0852667630 -0.20311700 0.24544874 0.10691293 -0.284444595 -0.27620982 -0.009992413 -0.15805341 -0.04069048 -0.58777097 -0.02720379 -0.051791865
HOLLMAN_APOPTOSIS_VIA_CD40_UP 0.159694118 0.0410536329 0.308668575 -0.12645484 -0.135319598 0.081107747 -0.319683205 -0.15899857 -0.16425438 0.0416693122 0.39281210 0.37753381 -0.13823891 0.167054476 -0.09557144 -0.123686107 -0.08994822 0.05111214 -0.33152469 0.33937060 -0.276396548
LIU_PROSTATE_CANCER_UP -0.200174601 -0.1024275640 -0.362769398 0.09620792 0.099175486 -0.064794023 0.327178382 0.18176145 0.14724468 -0.0478676575 -0.19636413 -0.37273481 0.06123468 -0.211530468 0.12140292 0.145476074 0.12739982 -0.13649384 0.35560281 -0.30529388 0.337766146
LIU_SOX4_TARGETS_UP -0.311115716 -0.0150999573 -0.370183270 0.02994648 0.007097133 -0.143160600 0.033179407 0.07347206 0.18075497 -0.0490631058 -0.13686508 -0.32569959 -0.04179661 0.071504493 0.25096389 0.077471847 0.21601436 -0.10244245 0.56524112 -0.25566844 0.245449068
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP -0.003982591 -0.0048376318 -0.110590132 0.20962500 0.165784093 0.006158587 0.461154480 0.14141161 0.13438601 0.0139659018 -0.51453201 -0.21847873 0.16418941 -0.369435533 -0.08635541 0.116735516 -0.02053522 0.03207892 -0.02647942 -0.32984473 0.239581866
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP 0.196501118 0.1026796537 0.240480585 -0.18619747 -0.078668907 0.006782133 -0.396278177 -0.06026344 -0.13359799 0.0137103217 0.25372378 0.31124485 0.02798112 0.261278988 -0.08560173 -0.168912257 -0.14454218 0.15143993 -0.35932984 0.36523086 -0.317661358
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP 0.195155486 0.0436878545 0.283825023 -0.19057341 -0.128414352 0.126639281 -0.230096834 -0.11125278 -0.16040060 0.0141769764 0.33836970 0.39001187 -0.06716428 0.242054659 -0.11258298 -0.266989610 -0.20349225 0.11360442 -0.30398607 0.29530770 -0.267879809
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP -0.294986347 0.0052927646 -0.356404299 0.11700956 -0.007887195 -0.086973052 -0.119261750 0.11415343 0.18703738 -0.0850102920 -0.05905421 -0.22051299 -0.13333692 0.063606967 0.29966264 -0.048516693 0.20245527 -0.07809657 0.67318459 -0.16966935 -0.002692925
FRASOR_TAMOXIFEN_RESPONSE_UP 0.188023524 0.0671210477 0.343491341 -0.07224244 0.049987182 0.005442805 -0.302414575 -0.05126835 -0.11773410 -0.0005034533 0.35344430 0.32597292 0.01419023 0.117754298 -0.16043707 -0.220436563 -0.20630553 0.12176178 -0.41686194 0.27627834 -0.315263740
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP 0.241880857 0.0105397235 0.347036800 -0.05973739 -0.062325297 0.069763158 -0.244608962 -0.06881315 -0.15614365 0.0243455638 0.35066650 0.32051680 -0.08383109 0.163672422 -0.15691721 -0.160817100 -0.21680375 0.08005991 -0.37514696 0.31594804 -0.339285197
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP -0.047998545 -0.0323723167 -0.060572908 0.16022173 0.275719671 -0.057408832 0.361535917 0.10716517 0.09414650 0.1002458630 -0.70393793 -0.26211976 0.25219492 -0.157844533 -0.09582946 0.126761665 -0.02440087 0.04045981 -0.07101498 -0.14668627 0.141735147
WATANABE_COLON_CANCER_MSI_VS_MSS_UP 0.201880848 0.0196443300 0.365010142 -0.11550445 -0.138797871 0.055947801 -0.007487674 -0.08694755 -0.14910284 0.0015427813 0.05838620 0.34951692 0.23248606 -0.088092361 -0.22754227 0.010672324 -0.19455170 0.13708637 -0.54111765 0.34525759 -0.228287022
SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP 0.013311652 -0.0003007427 0.023933970 0.16533251 0.319064898 -0.095372252 0.334778888 0.07494605 0.08931846 0.1961254232 -0.72402030 -0.14988899 0.22108366 -0.172773667 -0.14558504 0.074353483 -0.02784261 0.06165634 -0.17637553 -0.09439616 0.012649956
GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP -0.232713928 -0.1231571531 -0.436437041 0.03317630 0.055894544 0.009764435 0.173788487 0.07191884 0.11197173 -0.0962980513 -0.11688596 -0.28262921 -0.07519009 -0.009788198 0.31897933 0.099158027 0.14456325 -0.10034534 0.55453314 -0.29946776 0.199164634
>
GSVA.Rcheck/tests/test_ssgsea_newapi.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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>
> ## 2025-11-12 regression test script for method ssGSEA
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(geneprotExpCostaEtAl2021)
>
> set.seed(2025-11-12)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 -0.1065910 0.076987224 -1.3963246 1.2771019 -0.3372823
g2 1.6144451 0.006987175 1.2139285 0.9773345 0.2874821
g3 1.3882628 -0.690659025 -2.0385616 0.2804193 -0.1822753
g4 0.7027778 0.562919910 -0.1736422 0.3117396 0.3527060
g5 2.2575002 0.199992976 -0.4118118 0.1876944 0.2664025
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> ssgseaPar <- ssgseaParam(X, gs)
> ssgsea.es <- gsva(ssgseaPar, verbose=FALSE)
> dim(ssgsea.es)
[1] 100 30
> ssgsea.es[seq.int(min(nRowsToPrint, nrow(ssgsea.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 0.195744497 -0.007492004 0.301600527 0.185474518 -0.18513788 0.149750785 0.104235158 0.21982582 -0.04059905 0.0546902758 0.080490853 0.01193587 -0.189078543 0.19586020 0.14187966 0.243857036 0.28773234 0.217201774 0.089898831 0.116214343 0.173302995 0.1904137515 0.004424473 -0.02057674 0.098675842 -0.002447799 0.2303481731 0.035188821 0.24921715 0.02207138
gs2 0.173787356 0.215288246 0.081064338 0.197058309 0.18539426 0.064429420 0.049054913 0.04383380 0.24537648 0.1427741167 0.113136524 0.19607301 0.235574924 0.17122722 0.13185954 0.123028653 0.17177599 0.009941501 0.303178192 0.117202023 0.068318123 0.0046346956 0.256804756 0.09827169 0.019195345 0.105356826 0.0709289734 0.187662233 0.21904696 0.25162782
gs3 0.100242990 0.214266535 0.025346598 0.121799509 0.02314402 0.185547443 0.247378018 0.22176301 0.05615614 0.2199184542 0.150210558 0.12141509 0.041390591 0.17185644 0.16712379 0.160800994 0.12253414 0.138146897 0.169063790 0.123119082 0.177866072 0.1129259504 0.176262653 0.10362250 0.062898424 -0.038858962 0.0648894669 0.216703905 0.06399533 0.16468044
gs4 0.020219012 0.184283208 0.207467117 0.112328143 0.14232426 0.109864474 0.117292226 0.16062784 0.14894192 0.1099241598 0.109748655 0.15746660 0.123125813 0.13302212 0.16763188 0.149729866 0.05763524 0.173553145 0.212723927 0.006892486 0.092135828 0.0500747496 -0.008231010 0.13784400 0.078264303 0.074421255 0.2339312979 0.081848418 0.07206734 0.18302411
gs5 0.186960242 0.137355505 0.164176575 0.080281109 0.21776448 0.094783684 0.140854232 0.27335208 0.01701581 0.1690704205 0.196234294 -0.01297289 0.048753018 0.13879829 0.06248978 0.071929407 0.08349127 0.069867135 0.028650629 0.133924768 0.290422325 0.2318937904 0.222502179 0.10735534 0.288157755 0.176572685 0.2332335394 -0.020403838 0.10613574 0.20641671
gs6 0.084695350 0.129473129 -0.004340378 0.181252431 0.17126372 0.172715014 -0.053799216 0.09766095 0.29141114 -0.0548158144 0.099672139 0.14300115 0.308904034 0.23358662 0.12523153 0.222535617 -0.01026188 0.173978855 0.291953298 0.277291891 0.107406523 0.1822560230 0.210269980 0.24647535 0.124730021 0.068123708 0.3114158789 0.103249538 -0.03774461 0.15354838
gs7 -0.006439894 -0.018375473 0.176222210 0.136642887 0.11805896 0.024972385 0.103417953 0.18005687 0.08760701 0.0965303465 0.255123415 0.04459498 0.007120811 0.18947607 0.03611722 0.052402837 0.21080597 -0.092241631 0.116716432 0.215557790 -0.026615150 0.2010605090 0.078348467 0.13746060 0.124580215 0.134250350 0.2088376105 0.205407627 0.05985123 0.16835771
gs8 0.152548681 0.122036977 0.128210574 0.079535481 0.15438630 0.007725192 0.243321929 -0.01739644 0.18100507 0.1214663350 0.120563501 0.29581528 0.236166921 0.13943391 0.18990099 0.108444228 0.10471706 0.065349225 0.048151080 0.106494602 0.143364373 0.0534003280 0.128391744 0.13283415 0.213719804 0.224011101 0.0811281831 0.155087048 0.07400723 0.19907932
gs9 0.138073030 -0.070226176 -0.024824340 0.002543883 0.19231855 0.112075847 0.107012990 0.10994072 0.27932901 0.0402568193 0.062524777 0.12977595 0.173168014 0.16799103 0.18946682 0.201855705 0.04230591 0.020455909 0.056242387 0.048878490 0.082352941 -0.0023842520 0.001643744 0.19811479 0.335806700 0.225921081 0.1125303636 0.125208254 0.06132140 0.05988984
gs10 0.193002954 0.120468823 0.104541384 0.125361894 0.06434667 0.132647846 0.210099476 0.04340603 0.13245347 0.1816695429 0.029689089 0.04322589 0.136081364 0.02927292 0.16228975 0.137027690 0.04886648 0.157397521 0.103050592 0.177491442 0.145708075 0.1792860395 0.149847629 0.19708941 0.100952177 0.116207128 0.0310655770 0.075124821 0.29852738 0.04897969
gs11 0.050169605 0.132550037 0.169531128 0.210345302 0.19002363 0.158175843 0.244942291 0.18626305 0.10573317 0.0551313491 0.105236463 0.17399437 0.183985184 0.06912979 0.18520559 0.057598886 0.06228288 0.024420834 0.126270457 0.292532686 0.008052765 0.0868292384 0.258117853 0.26247578 0.220619090 0.128095043 0.1567157464 0.290712340 0.09113413 0.25482379
gs12 0.150921510 0.193900610 0.139316951 0.139247536 0.02507073 -0.014461477 0.081153890 0.12648602 0.36227771 0.1610782224 0.144927517 -0.01610972 0.303094010 0.13761564 0.13760078 0.234845397 0.20393239 0.124983017 -0.100636883 -0.037354816 0.205447937 0.0846989902 -0.065090416 0.19984798 0.067893453 -0.039196594 0.0570222320 0.068322400 0.23402799 0.13246560
gs13 0.195510100 -0.066299953 0.247912207 0.150833170 0.20537547 0.144116338 0.139669933 0.11691800 0.12623331 0.0807671865 0.002752369 0.20632767 0.057972383 0.23913100 0.03736037 0.028874447 0.16271844 0.055835246 0.069509854 0.006508768 0.305296167 0.1264768537 0.160884957 0.19250108 0.367609534 0.098173015 0.2138200910 0.095696541 0.11802246 0.13408982
gs14 -0.079338005 0.132016907 0.073594075 0.133467362 0.20868580 0.120123546 -0.027647545 0.07595014 0.11777690 0.1681301315 -0.005407843 0.05423839 0.066372111 0.04432401 0.12775476 0.006190328 0.16787819 0.165826628 0.122710278 0.047787684 0.091901140 0.1352975702 0.136800236 0.04922752 0.270510964 0.279393636 0.0588397736 0.221855365 0.17013841 0.19316373
gs15 0.048721243 0.070204063 -0.255809492 0.003739553 0.14475443 0.452404332 0.279085197 -0.02388306 0.24294570 0.0726393170 0.129721333 -0.03093770 -0.316561037 0.40489146 0.09668840 0.438502742 0.09011458 0.180191668 -0.002063173 0.088601756 -0.028951316 0.0592235553 -0.023049429 0.05517510 0.065859334 0.169886617 -0.0210843810 0.239990760 0.11376404 0.26036345
gs16 0.242723731 0.033766662 0.162335972 0.134048541 0.27953498 0.333815994 -0.044517962 0.01960052 0.36026405 0.0824516518 -0.022131056 0.12994241 0.201016108 -0.16875550 -0.02200338 -0.096595349 0.05089660 -0.067384917 0.263489359 -0.084887470 -0.122517223 0.1853698050 0.106513225 0.13938004 0.204697570 0.301740983 0.3991276260 0.241717505 -0.07191537 0.06447749
gs17 0.089661560 0.182462506 0.095291134 0.123652944 0.16585174 0.148418510 0.259786477 0.19755038 0.12832194 0.1180470269 0.116130415 0.19829278 0.006146566 0.21599987 0.17922731 0.240188128 0.09907450 0.076120677 0.112565771 0.134321406 0.213513143 0.0795473135 0.105870946 0.23277452 0.128079921 0.126322427 0.0895096262 0.206529009 0.19940855 0.15232017
gs18 0.117672382 -0.003135810 0.224156275 0.168487836 0.04835594 0.210008127 0.036035332 0.17341528 0.11176881 0.1981711657 0.276694912 -0.01739321 0.174476328 0.22877659 0.06531119 0.084359867 0.21821342 0.043098382 0.177808186 0.108343091 0.156021210 0.1118170410 0.095286458 0.22722303 0.270933413 0.041262967 0.0009571424 0.006945131 0.10697023 0.30378672
gs19 0.124473444 0.230715598 0.206660042 0.140461653 0.05571301 0.064779518 0.088143782 0.19935035 0.18345133 0.1888584049 0.142867773 0.12853605 0.116502743 0.03700926 0.21067102 0.169657387 0.19355914 0.250254169 0.189424694 0.022383546 0.045633053 0.1379770166 0.190052180 0.12776225 0.199958385 0.136566882 0.1753586463 0.289675459 0.14674136 0.17374162
gs20 0.186582210 0.100760638 -0.095827792 0.295359930 0.09483376 0.240818176 0.003665823 0.38273093 -0.22311923 0.2024333438 0.138424243 0.03656744 0.178476843 0.22886900 0.19526099 -0.067067145 -0.21949316 0.136292263 -0.201602573 0.349858031 -0.059289500 0.0141583858 0.199922590 -0.01276828 0.546102276 0.152227491 0.1340483654 0.253737161 0.01693072 0.28198677
gs21 0.067922340 0.045855471 0.223399593 0.111091740 0.09584298 0.345990073 0.332540749 0.19762161 0.14469915 0.0937296970 0.075390216 0.32005981 0.045172541 0.07046626 0.20879671 0.022627948 0.26105687 0.059012562 0.292398840 0.354364818 -0.090550177 0.0001911735 -0.079833523 0.19746685 -0.001287554 0.450260158 0.0312719372 0.094489792 0.10325559 0.30632075
gs22 0.013212615 0.145069065 0.084014215 0.115932415 0.37824881 0.103012907 0.164589872 -0.01369833 0.10510038 0.1335330309 0.179746071 0.26896103 -0.073924527 0.02210166 0.22325299 0.288735769 0.17182569 0.024231335 0.015533650 0.235958807 0.039508938 -0.0103720320 -0.018274220 -0.15082170 -0.047863512 0.218450885 0.1553436400 0.124602687 0.23689850 0.24716375
gs23 0.198642947 0.188136367 0.220069138 0.250655020 0.24913061 0.092218274 0.098429214 0.23869243 0.08622866 -0.0545559911 0.165403416 0.00209425 0.330074431 0.20563943 0.36114162 0.143011222 -0.01274591 0.118839748 0.145486749 0.184722739 0.056565164 0.1542018599 0.246112711 0.02044637 0.168976343 0.240083494 0.1081100291 0.077070629 0.13622744 0.04629302
gs24 0.281022110 0.112102895 0.172521000 0.023216741 0.31371250 -0.106544386 -0.202642330 0.13901406 0.39053781 -0.0004772649 -0.106785138 0.19626618 0.167473789 -0.05035892 0.12542447 0.228387328 0.45317849 -0.058261877 0.517121440 0.249113807 0.170409424 0.0456422403 0.137742530 0.12193577 -0.251058686 0.041923351 0.0181378566 0.172167349 0.39523206 -0.44541507
gs25 0.223669975 0.228317312 0.286003981 0.079225905 0.32461076 0.138825171 -0.012500931 0.31143887 0.30481063 0.2771794275 0.088644514 0.31099700 0.068792248 0.15198294 -0.03305703 0.172289819 0.14104334 0.361741589 0.003150102 0.131935206 0.345958821 0.0220911019 0.050584792 0.20036063 -0.027507264 0.056624711 0.0199252149 -0.033997869 0.15512914 0.27730945
>
> c2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> firPar <- ssgseaParam(geneExpCostaEtAl2021, c2BroadSets,
+ minSize=10, maxSize=500)
ℹ No assay name provided; using default assay 'logCPM'
> fir_es <- gsva(firPar, verbose=FALSE)
> assay(fir_es)[seq.int(min(nRowsToPrint, nrow(fir_es))),]
BS03 BS04 BS05 BS06 BS07 BS08 BS09 BS10 BS11 BS12 BS13 BS14 BS16 BS17 BS18 BS19 BS20 BS21 BS22 BS23 BS24
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP -0.047861975 -0.064510514 -0.089755563 -0.133729578 -0.199868503 0.0026855672 -0.20391112 -0.093535842 -0.106377087 -0.13794493 0.19982323 -0.02598133 -0.177824702 -0.019819317 -0.027103154 -0.06731622 -0.026678997 -0.0973454800 -0.0073405382 -0.02571356 -0.090784952
WINTER_HYPOXIA_UP 0.083661174 0.104144600 0.075204536 0.088499880 0.082515892 0.1306230825 0.08511734 0.112800156 0.111315832 0.07815189 0.13650298 0.11704900 0.133661593 0.160540798 0.119855555 0.08879717 0.120941818 0.1117787200 0.1275813779 0.11310648 0.122788107
PARENT_MTOR_SIGNALING_UP 0.145097578 0.142260606 0.142582696 0.153082133 0.152217535 0.1484095311 0.16914247 0.153664158 0.149853782 0.14185395 0.13216072 0.14089724 0.165446859 0.138154449 0.130170039 0.15685130 0.141870809 0.1480114583 0.1311289317 0.14041853 0.154395223
PYEON_HPV_POSITIVE_TUMORS_UP 0.177698184 0.155498931 0.183390005 0.131442094 0.119809793 0.1487405099 0.13887716 0.127491215 0.137467608 0.15088270 0.23520263 0.20714881 0.076799786 0.082125526 0.151994389 0.10960057 0.132433657 0.1136252542 0.1291682046 0.11282144 0.123023244
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP 0.034288455 0.039235404 0.036407387 0.039519662 0.017458542 0.0478439590 0.01207432 0.043052771 0.047319392 0.03254125 0.12089813 0.05455612 0.031887232 0.075515119 0.068398279 0.05070747 0.069177581 0.0494085877 0.0853686370 0.06439365 0.055039548
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP 0.022116945 0.039419660 -0.015184316 -0.005173185 -0.008342259 -0.0036528816 -0.04682334 0.020172368 0.018001565 0.03533308 0.05640619 0.06242093 0.044256135 0.091113755 0.052485216 0.06696480 0.068440654 0.0104122457 0.0073292607 0.08353347 0.017870841
LU_TUMOR_VASCULATURE_UP 0.214125804 0.126289989 0.139835058 0.109624044 0.157218544 0.1812521798 0.16177130 0.134460408 0.118434708 0.09186298 0.13638652 0.16896511 0.163795407 0.187410200 0.094874801 0.13092418 0.181076988 0.1645530704 0.0703969305 0.21002848 0.093501387
KORKOLA_EMBRYONAL_CARCINOMA_UP 0.222009101 0.218986340 0.226201573 0.203592591 0.213050560 0.2250776962 0.20639969 0.217832038 0.217699103 0.23261778 0.28870156 0.24132429 0.194689427 0.229047467 0.234189560 0.22532409 0.227277907 0.2277982065 0.2177010289 0.24374401 0.224757948
KORKOLA_TERATOMA_UP 0.259686475 0.249105870 0.221616808 0.223085623 0.252072504 0.2143319888 0.23063320 0.227770380 0.206523649 0.23791626 0.24039542 0.22004326 0.218858165 0.201141034 0.191349234 0.21556406 0.185795916 0.2722283788 0.1346092761 0.23601301 0.181938159
KORKOLA_YOLK_SAC_TUMOR_UP 0.178619805 0.165040943 0.169704662 0.150542509 0.171407532 0.2122073051 0.20242910 0.160110157 0.170282871 0.19045199 0.24809274 0.17187660 0.139377189 0.194035609 0.191204846 0.19791442 0.179164160 0.2021771510 0.1878345566 0.19354696 0.193016387
KORKOLA_SEMINOMA_UP 0.133113484 0.136878486 0.138543898 0.126197935 0.141120519 0.1508717025 0.14415574 0.138314673 0.124871318 0.15393574 0.17770544 0.14322146 0.123027384 0.147081718 0.147116756 0.16616405 0.155138965 0.1519754681 0.1445937659 0.14337052 0.154180291
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP 0.269386658 0.268398024 0.268785087 0.264794524 0.257979385 0.2812819533 0.26715937 0.273530232 0.263428749 0.27210581 0.28879671 0.27399201 0.272532217 0.284858492 0.262268036 0.27832983 0.269027725 0.2849786663 0.2690840525 0.28354066 0.272301829
HOLLMAN_APOPTOSIS_VIA_CD40_UP 0.160359333 0.159826714 0.177145360 0.168534749 0.158880959 0.1931367813 0.17850109 0.189096381 0.186325235 0.18123834 0.20817697 0.16424378 0.177961003 0.191630608 0.189819707 0.18885847 0.190932749 0.1888250959 0.1920117340 0.19419261 0.194871879
LIU_PROSTATE_CANCER_UP -0.001686653 -0.015511745 -0.003665841 -0.008981589 -0.014862771 0.0188483587 -0.04421093 -0.012124533 -0.015498855 -0.01135793 0.05110251 0.00589405 -0.025071646 0.012062704 0.015131473 -0.01755863 0.004792661 0.0003175159 0.0007877954 0.02295983 -0.004175563
LIU_SOX4_TARGETS_UP 0.266579362 0.269431395 0.268564256 0.267174629 0.261257831 0.2598944519 0.25093626 0.271206262 0.262487930 0.26869110 0.25003785 0.25670734 0.268391432 0.267961889 0.262049592 0.26015729 0.261870318 0.2731214332 0.2515318624 0.27003163 0.255185999
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP 0.146753519 0.124600931 0.121215340 0.128974181 0.133245736 0.1370355801 0.15494493 0.135989367 0.129229042 0.13295527 0.13753602 0.11798662 0.134128220 0.122367316 0.111147464 0.14444211 0.126454769 0.1477499094 0.1018495860 0.12346761 0.143982712
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP 0.207394854 0.204495809 0.194833703 0.193839193 0.195221037 0.1793697936 0.15165961 0.190721684 0.193657583 0.20911487 0.22115938 0.20690448 0.208970600 0.219336099 0.192192509 0.22617085 0.210900404 0.2253846653 0.1588932578 0.24428677 0.176022016
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP 0.149133829 0.161658078 0.137075328 0.158420525 0.172941123 0.1781333198 0.12770095 0.131425925 0.163910913 0.16421183 0.09148373 0.17413757 0.174918166 0.161035432 0.129100373 0.19853351 0.183619956 0.1557244736 0.1386831218 0.17554895 0.176162745
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP 0.240266307 0.253979353 0.222799455 0.272617073 0.247850918 0.2995380936 0.25649343 0.284974209 0.286365886 0.22519134 0.23159537 0.25398199 0.249316100 0.275511482 0.281062725 0.29408241 0.311864521 0.2462289005 0.3190743880 0.23332591 0.253909487
FRASOR_TAMOXIFEN_RESPONSE_UP 0.221842346 0.210310821 0.217796045 0.211107447 0.202213645 0.2102725800 0.19926671 0.207615561 0.215368600 0.22360807 0.20942112 0.21421355 0.209381560 0.201311092 0.197792727 0.24605384 0.227865607 0.2283649413 0.1984246557 0.24245709 0.203786006
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP -0.060426507 -0.004891786 -0.072765554 -0.026368501 -0.016115879 -0.0006868769 -0.06008843 -0.002537486 0.005236499 -0.05545551 -0.02121140 -0.01190172 0.003087601 0.042319548 0.017767010 -0.01618425 -0.024243782 0.0137988384 0.0299928703 -0.01925669 0.014508147
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP 0.147208423 0.129565672 0.127656438 0.113452808 0.092707187 0.1159546589 0.06265690 0.114868203 0.117516428 0.11916643 0.26156789 0.16071737 0.077231868 0.138553483 0.154515458 0.10565995 0.136555397 0.1137143968 0.1409631836 0.13575878 0.103254762
WATANABE_COLON_CANCER_MSI_VS_MSS_UP 0.204823558 0.244893394 0.214889080 0.270801271 0.240099497 0.2234094239 0.23373349 0.224114103 0.248118001 0.23397207 0.27896785 0.23449799 0.252781687 0.215628124 0.233426813 0.27229523 0.268769194 0.2517617395 0.2368230900 0.22577370 0.263727538
SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP -0.076663968 -0.064558807 -0.093788571 -0.102411098 -0.139873649 -0.0457729741 -0.16603431 -0.066533913 -0.076129915 -0.11891191 0.19010928 -0.02884104 -0.123643922 -0.009501277 -0.002395499 -0.09928048 -0.046946835 -0.0854818844 0.0243023758 -0.05452892 -0.071302803
GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP 0.165921843 0.146439546 0.173083699 0.150887049 0.149471957 0.1345982868 0.13133671 0.153614793 0.156904617 0.14680764 0.13915461 0.18299481 0.146975954 0.155398130 0.126696824 0.15081078 0.138603009 0.1623655660 0.1023378923 0.17293499 0.129406847
>
> proc.time()
user system elapsed
6.356 0.230 6.936
GSVA.Rcheck/tests/test_ssgsea_newapi.Rout.save
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>
> ## 2025-11-12 regression test script for method ssGSEA
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(geneprotExpCostaEtAl2021)
>
> set.seed(2025-11-12)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 -0.1065910 0.076987224 -1.3963246 1.2771019 -0.3372823
g2 1.6144451 0.006987175 1.2139285 0.9773345 0.2874821
g3 1.3882628 -0.690659025 -2.0385616 0.2804193 -0.1822753
g4 0.7027778 0.562919910 -0.1736422 0.3117396 0.3527060
g5 2.2575002 0.199992976 -0.4118118 0.1876944 0.2664025
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> ssgseaPar <- ssgseaParam(X, gs)
> ssgsea.es <- gsva(ssgseaPar, verbose=FALSE)
> dim(ssgsea.es)
[1] 100 30
> ssgsea.es[seq.int(min(nRowsToPrint, nrow(ssgsea.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 0.195744497 -0.007492004 0.301600527 0.185474518 -0.18513788 0.149750785 0.104235158 0.21982582 -0.04059905 0.0546902758 0.080490853 0.01193587 -0.189078543 0.19586020 0.14187966 0.243857036 0.28773234 0.217201774 0.089898831 0.116214343 0.173302995 0.1904137515 0.004424473 -0.02057674 0.098675842 -0.002447799 0.2303481731 0.035188821 0.24921715 0.02207138
gs2 0.173787356 0.215288246 0.081064338 0.197058309 0.18539426 0.064429420 0.049054913 0.04383380 0.24537648 0.1427741167 0.113136524 0.19607301 0.235574924 0.17122722 0.13185954 0.123028653 0.17177599 0.009941501 0.303178192 0.117202023 0.068318123 0.0046346956 0.256804756 0.09827169 0.019195345 0.105356826 0.0709289734 0.187662233 0.21904696 0.25162782
gs3 0.100242990 0.214266535 0.025346598 0.121799509 0.02314402 0.185547443 0.247378018 0.22176301 0.05615614 0.2199184542 0.150210558 0.12141509 0.041390591 0.17185644 0.16712379 0.160800994 0.12253414 0.138146897 0.169063790 0.123119082 0.177866072 0.1129259504 0.176262653 0.10362250 0.062898424 -0.038858962 0.0648894669 0.216703905 0.06399533 0.16468044
gs4 0.020219012 0.184283208 0.207467117 0.112328143 0.14232426 0.109864474 0.117292226 0.16062784 0.14894192 0.1099241598 0.109748655 0.15746660 0.123125813 0.13302212 0.16763188 0.149729866 0.05763524 0.173553145 0.212723927 0.006892486 0.092135828 0.0500747496 -0.008231010 0.13784400 0.078264303 0.074421255 0.2339312979 0.081848418 0.07206734 0.18302411
gs5 0.186960242 0.137355505 0.164176575 0.080281109 0.21776448 0.094783684 0.140854232 0.27335208 0.01701581 0.1690704205 0.196234294 -0.01297289 0.048753018 0.13879829 0.06248978 0.071929407 0.08349127 0.069867135 0.028650629 0.133924768 0.290422325 0.2318937904 0.222502179 0.10735534 0.288157755 0.176572685 0.2332335394 -0.020403838 0.10613574 0.20641671
gs6 0.084695350 0.129473129 -0.004340378 0.181252431 0.17126372 0.172715014 -0.053799216 0.09766095 0.29141114 -0.0548158144 0.099672139 0.14300115 0.308904034 0.23358662 0.12523153 0.222535617 -0.01026188 0.173978855 0.291953298 0.277291891 0.107406523 0.1822560230 0.210269980 0.24647535 0.124730021 0.068123708 0.3114158789 0.103249538 -0.03774461 0.15354838
gs7 -0.006439894 -0.018375473 0.176222210 0.136642887 0.11805896 0.024972385 0.103417953 0.18005687 0.08760701 0.0965303465 0.255123415 0.04459498 0.007120811 0.18947607 0.03611722 0.052402837 0.21080597 -0.092241631 0.116716432 0.215557790 -0.026615150 0.2010605090 0.078348467 0.13746060 0.124580215 0.134250350 0.2088376105 0.205407627 0.05985123 0.16835771
gs8 0.152548681 0.122036977 0.128210574 0.079535481 0.15438630 0.007725192 0.243321929 -0.01739644 0.18100507 0.1214663350 0.120563501 0.29581528 0.236166921 0.13943391 0.18990099 0.108444228 0.10471706 0.065349225 0.048151080 0.106494602 0.143364373 0.0534003280 0.128391744 0.13283415 0.213719804 0.224011101 0.0811281831 0.155087048 0.07400723 0.19907932
gs9 0.138073030 -0.070226176 -0.024824340 0.002543883 0.19231855 0.112075847 0.107012990 0.10994072 0.27932901 0.0402568193 0.062524777 0.12977595 0.173168014 0.16799103 0.18946682 0.201855705 0.04230591 0.020455909 0.056242387 0.048878490 0.082352941 -0.0023842520 0.001643744 0.19811479 0.335806700 0.225921081 0.1125303636 0.125208254 0.06132140 0.05988984
gs10 0.193002954 0.120468823 0.104541384 0.125361894 0.06434667 0.132647846 0.210099476 0.04340603 0.13245347 0.1816695429 0.029689089 0.04322589 0.136081364 0.02927292 0.16228975 0.137027690 0.04886648 0.157397521 0.103050592 0.177491442 0.145708075 0.1792860395 0.149847629 0.19708941 0.100952177 0.116207128 0.0310655770 0.075124821 0.29852738 0.04897969
gs11 0.050169605 0.132550037 0.169531128 0.210345302 0.19002363 0.158175843 0.244942291 0.18626305 0.10573317 0.0551313491 0.105236463 0.17399437 0.183985184 0.06912979 0.18520559 0.057598886 0.06228288 0.024420834 0.126270457 0.292532686 0.008052765 0.0868292384 0.258117853 0.26247578 0.220619090 0.128095043 0.1567157464 0.290712340 0.09113413 0.25482379
gs12 0.150921510 0.193900610 0.139316951 0.139247536 0.02507073 -0.014461477 0.081153890 0.12648602 0.36227771 0.1610782224 0.144927517 -0.01610972 0.303094010 0.13761564 0.13760078 0.234845397 0.20393239 0.124983017 -0.100636883 -0.037354816 0.205447937 0.0846989902 -0.065090416 0.19984798 0.067893453 -0.039196594 0.0570222320 0.068322400 0.23402799 0.13246560
gs13 0.195510100 -0.066299953 0.247912207 0.150833170 0.20537547 0.144116338 0.139669933 0.11691800 0.12623331 0.0807671865 0.002752369 0.20632767 0.057972383 0.23913100 0.03736037 0.028874447 0.16271844 0.055835246 0.069509854 0.006508768 0.305296167 0.1264768537 0.160884957 0.19250108 0.367609534 0.098173015 0.2138200910 0.095696541 0.11802246 0.13408982
gs14 -0.079338005 0.132016907 0.073594075 0.133467362 0.20868580 0.120123546 -0.027647545 0.07595014 0.11777690 0.1681301315 -0.005407843 0.05423839 0.066372111 0.04432401 0.12775476 0.006190328 0.16787819 0.165826628 0.122710278 0.047787684 0.091901140 0.1352975702 0.136800236 0.04922752 0.270510964 0.279393636 0.0588397736 0.221855365 0.17013841 0.19316373
gs15 0.048721243 0.070204063 -0.255809492 0.003739553 0.14475443 0.452404332 0.279085197 -0.02388306 0.24294570 0.0726393170 0.129721333 -0.03093770 -0.316561037 0.40489146 0.09668840 0.438502742 0.09011458 0.180191668 -0.002063173 0.088601756 -0.028951316 0.0592235553 -0.023049429 0.05517510 0.065859334 0.169886617 -0.0210843810 0.239990760 0.11376404 0.26036345
gs16 0.242723731 0.033766662 0.162335972 0.134048541 0.27953498 0.333815994 -0.044517962 0.01960052 0.36026405 0.0824516518 -0.022131056 0.12994241 0.201016108 -0.16875550 -0.02200338 -0.096595349 0.05089660 -0.067384917 0.263489359 -0.084887470 -0.122517223 0.1853698050 0.106513225 0.13938004 0.204697570 0.301740983 0.3991276260 0.241717505 -0.07191537 0.06447749
gs17 0.089661560 0.182462506 0.095291134 0.123652944 0.16585174 0.148418510 0.259786477 0.19755038 0.12832194 0.1180470269 0.116130415 0.19829278 0.006146566 0.21599987 0.17922731 0.240188128 0.09907450 0.076120677 0.112565771 0.134321406 0.213513143 0.0795473135 0.105870946 0.23277452 0.128079921 0.126322427 0.0895096262 0.206529009 0.19940855 0.15232017
gs18 0.117672382 -0.003135810 0.224156275 0.168487836 0.04835594 0.210008127 0.036035332 0.17341528 0.11176881 0.1981711657 0.276694912 -0.01739321 0.174476328 0.22877659 0.06531119 0.084359867 0.21821342 0.043098382 0.177808186 0.108343091 0.156021210 0.1118170410 0.095286458 0.22722303 0.270933413 0.041262967 0.0009571424 0.006945131 0.10697023 0.30378672
gs19 0.124473444 0.230715598 0.206660042 0.140461653 0.05571301 0.064779518 0.088143782 0.19935035 0.18345133 0.1888584049 0.142867773 0.12853605 0.116502743 0.03700926 0.21067102 0.169657387 0.19355914 0.250254169 0.189424694 0.022383546 0.045633053 0.1379770166 0.190052180 0.12776225 0.199958385 0.136566882 0.1753586463 0.289675459 0.14674136 0.17374162
gs20 0.186582210 0.100760638 -0.095827792 0.295359930 0.09483376 0.240818176 0.003665823 0.38273093 -0.22311923 0.2024333438 0.138424243 0.03656744 0.178476843 0.22886900 0.19526099 -0.067067145 -0.21949316 0.136292263 -0.201602573 0.349858031 -0.059289500 0.0141583858 0.199922590 -0.01276828 0.546102276 0.152227491 0.1340483654 0.253737161 0.01693072 0.28198677
gs21 0.067922340 0.045855471 0.223399593 0.111091740 0.09584298 0.345990073 0.332540749 0.19762161 0.14469915 0.0937296970 0.075390216 0.32005981 0.045172541 0.07046626 0.20879671 0.022627948 0.26105687 0.059012562 0.292398840 0.354364818 -0.090550177 0.0001911735 -0.079833523 0.19746685 -0.001287554 0.450260158 0.0312719372 0.094489792 0.10325559 0.30632075
gs22 0.013212615 0.145069065 0.084014215 0.115932415 0.37824881 0.103012907 0.164589872 -0.01369833 0.10510038 0.1335330309 0.179746071 0.26896103 -0.073924527 0.02210166 0.22325299 0.288735769 0.17182569 0.024231335 0.015533650 0.235958807 0.039508938 -0.0103720320 -0.018274220 -0.15082170 -0.047863512 0.218450885 0.1553436400 0.124602687 0.23689850 0.24716375
gs23 0.198642947 0.188136367 0.220069138 0.250655020 0.24913061 0.092218274 0.098429214 0.23869243 0.08622866 -0.0545559911 0.165403416 0.00209425 0.330074431 0.20563943 0.36114162 0.143011222 -0.01274591 0.118839748 0.145486749 0.184722739 0.056565164 0.1542018599 0.246112711 0.02044637 0.168976343 0.240083494 0.1081100291 0.077070629 0.13622744 0.04629302
gs24 0.281022110 0.112102895 0.172521000 0.023216741 0.31371250 -0.106544386 -0.202642330 0.13901406 0.39053781 -0.0004772649 -0.106785138 0.19626618 0.167473789 -0.05035892 0.12542447 0.228387328 0.45317849 -0.058261877 0.517121440 0.249113807 0.170409424 0.0456422403 0.137742530 0.12193577 -0.251058686 0.041923351 0.0181378566 0.172167349 0.39523206 -0.44541507
gs25 0.223669975 0.228317312 0.286003981 0.079225905 0.32461076 0.138825171 -0.012500931 0.31143887 0.30481063 0.2771794275 0.088644514 0.31099700 0.068792248 0.15198294 -0.03305703 0.172289819 0.14104334 0.361741589 0.003150102 0.131935206 0.345958821 0.0220911019 0.050584792 0.20036063 -0.027507264 0.056624711 0.0199252149 -0.033997869 0.15512914 0.27730945
>
> c2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> firPar <- ssgseaParam(geneExpCostaEtAl2021, c2BroadSets,
+ minSize=10, maxSize=500)
ℹ No assay name provided; using default assay 'logCPM'
> fir_es <- gsva(firPar, verbose=FALSE)
> assay(fir_es)[seq.int(min(nRowsToPrint, nrow(fir_es))),]
BS03 BS04 BS05 BS06 BS07 BS08 BS09 BS10 BS11 BS12 BS13 BS14 BS16 BS17 BS18 BS19 BS20 BS21 BS22 BS23 BS24
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP -0.047861975 -0.064510514 -0.089755563 -0.133729578 -0.199868503 0.0026855672 -0.20391112 -0.093535842 -0.106377087 -0.13794493 0.19982323 -0.02598133 -0.177824702 -0.019819317 -0.027103154 -0.06731622 -0.026678997 -0.0973454800 -0.0073405382 -0.02571356 -0.090784952
WINTER_HYPOXIA_UP 0.083661174 0.104144600 0.075204536 0.088499880 0.082515892 0.1306230825 0.08511734 0.112800156 0.111315832 0.07815189 0.13650298 0.11704900 0.133661593 0.160540798 0.119855555 0.08879717 0.120941818 0.1117787200 0.1275813779 0.11310648 0.122788107
PARENT_MTOR_SIGNALING_UP 0.145097578 0.142260606 0.142582696 0.153082133 0.152217535 0.1484095311 0.16914247 0.153664158 0.149853782 0.14185395 0.13216072 0.14089724 0.165446859 0.138154449 0.130170039 0.15685130 0.141870809 0.1480114583 0.1311289317 0.14041853 0.154395223
PYEON_HPV_POSITIVE_TUMORS_UP 0.177698184 0.155498931 0.183390005 0.131442094 0.119809793 0.1487405099 0.13887716 0.127491215 0.137467608 0.15088270 0.23520263 0.20714881 0.076799786 0.082125526 0.151994389 0.10960057 0.132433657 0.1136252542 0.1291682046 0.11282144 0.123023244
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP 0.034288455 0.039235404 0.036407387 0.039519662 0.017458542 0.0478439590 0.01207432 0.043052771 0.047319392 0.03254125 0.12089813 0.05455612 0.031887232 0.075515119 0.068398279 0.05070747 0.069177581 0.0494085877 0.0853686370 0.06439365 0.055039548
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP 0.022116945 0.039419660 -0.015184316 -0.005173185 -0.008342259 -0.0036528816 -0.04682334 0.020172368 0.018001565 0.03533308 0.05640619 0.06242093 0.044256135 0.091113755 0.052485216 0.06696480 0.068440654 0.0104122457 0.0073292607 0.08353347 0.017870841
LU_TUMOR_VASCULATURE_UP 0.214125804 0.126289989 0.139835058 0.109624044 0.157218544 0.1812521798 0.16177130 0.134460408 0.118434708 0.09186298 0.13638652 0.16896511 0.163795407 0.187410200 0.094874801 0.13092418 0.181076988 0.1645530704 0.0703969305 0.21002848 0.093501387
KORKOLA_EMBRYONAL_CARCINOMA_UP 0.222009101 0.218986340 0.226201573 0.203592591 0.213050560 0.2250776962 0.20639969 0.217832038 0.217699103 0.23261778 0.28870156 0.24132429 0.194689427 0.229047467 0.234189560 0.22532409 0.227277907 0.2277982065 0.2177010289 0.24374401 0.224757948
KORKOLA_TERATOMA_UP 0.259686475 0.249105870 0.221616808 0.223085623 0.252072504 0.2143319888 0.23063320 0.227770380 0.206523649 0.23791626 0.24039542 0.22004326 0.218858165 0.201141034 0.191349234 0.21556406 0.185795916 0.2722283788 0.1346092761 0.23601301 0.181938159
KORKOLA_YOLK_SAC_TUMOR_UP 0.178619805 0.165040943 0.169704662 0.150542509 0.171407532 0.2122073051 0.20242910 0.160110157 0.170282871 0.19045199 0.24809274 0.17187660 0.139377189 0.194035609 0.191204846 0.19791442 0.179164160 0.2021771510 0.1878345566 0.19354696 0.193016387
KORKOLA_SEMINOMA_UP 0.133113484 0.136878486 0.138543898 0.126197935 0.141120519 0.1508717025 0.14415574 0.138314673 0.124871318 0.15393574 0.17770544 0.14322146 0.123027384 0.147081718 0.147116756 0.16616405 0.155138965 0.1519754681 0.1445937659 0.14337052 0.154180291
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP 0.269386658 0.268398024 0.268785087 0.264794524 0.257979385 0.2812819533 0.26715937 0.273530232 0.263428749 0.27210581 0.28879671 0.27399201 0.272532217 0.284858492 0.262268036 0.27832983 0.269027725 0.2849786663 0.2690840525 0.28354066 0.272301829
HOLLMAN_APOPTOSIS_VIA_CD40_UP 0.160359333 0.159826714 0.177145360 0.168534749 0.158880959 0.1931367813 0.17850109 0.189096381 0.186325235 0.18123834 0.20817697 0.16424378 0.177961003 0.191630608 0.189819707 0.18885847 0.190932749 0.1888250959 0.1920117340 0.19419261 0.194871879
LIU_PROSTATE_CANCER_UP -0.001686653 -0.015511745 -0.003665841 -0.008981589 -0.014862771 0.0188483587 -0.04421093 -0.012124533 -0.015498855 -0.01135793 0.05110251 0.00589405 -0.025071646 0.012062704 0.015131473 -0.01755863 0.004792661 0.0003175159 0.0007877954 0.02295983 -0.004175563
LIU_SOX4_TARGETS_UP 0.266579362 0.269431395 0.268564256 0.267174629 0.261257831 0.2598944519 0.25093626 0.271206262 0.262487930 0.26869110 0.25003785 0.25670734 0.268391432 0.267961889 0.262049592 0.26015729 0.261870318 0.2731214332 0.2515318624 0.27003163 0.255185999
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP 0.146753519 0.124600931 0.121215340 0.128974181 0.133245736 0.1370355801 0.15494493 0.135989367 0.129229042 0.13295527 0.13753602 0.11798662 0.134128220 0.122367316 0.111147464 0.14444211 0.126454769 0.1477499094 0.1018495860 0.12346761 0.143982712
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP 0.207394854 0.204495809 0.194833703 0.193839193 0.195221037 0.1793697936 0.15165961 0.190721684 0.193657583 0.20911487 0.22115938 0.20690448 0.208970600 0.219336099 0.192192509 0.22617085 0.210900404 0.2253846653 0.1588932578 0.24428677 0.176022016
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP 0.149133829 0.161658078 0.137075328 0.158420525 0.172941123 0.1781333198 0.12770095 0.131425925 0.163910913 0.16421183 0.09148373 0.17413757 0.174918166 0.161035432 0.129100373 0.19853351 0.183619956 0.1557244736 0.1386831218 0.17554895 0.176162745
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP 0.240266307 0.253979353 0.222799455 0.272617073 0.247850918 0.2995380936 0.25649343 0.284974209 0.286365886 0.22519134 0.23159537 0.25398199 0.249316100 0.275511482 0.281062725 0.29408241 0.311864521 0.2462289005 0.3190743880 0.23332591 0.253909487
FRASOR_TAMOXIFEN_RESPONSE_UP 0.221842346 0.210310821 0.217796045 0.211107447 0.202213645 0.2102725800 0.19926671 0.207615561 0.215368600 0.22360807 0.20942112 0.21421355 0.209381560 0.201311092 0.197792727 0.24605384 0.227865607 0.2283649413 0.1984246557 0.24245709 0.203786006
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP -0.060426507 -0.004891786 -0.072765554 -0.026368501 -0.016115879 -0.0006868769 -0.06008843 -0.002537486 0.005236499 -0.05545551 -0.02121140 -0.01190172 0.003087601 0.042319548 0.017767010 -0.01618425 -0.024243782 0.0137988384 0.0299928703 -0.01925669 0.014508147
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP 0.147208423 0.129565672 0.127656438 0.113452808 0.092707187 0.1159546589 0.06265690 0.114868203 0.117516428 0.11916643 0.26156789 0.16071737 0.077231868 0.138553483 0.154515458 0.10565995 0.136555397 0.1137143968 0.1409631836 0.13575878 0.103254762
WATANABE_COLON_CANCER_MSI_VS_MSS_UP 0.204823558 0.244893394 0.214889080 0.270801271 0.240099497 0.2234094239 0.23373349 0.224114103 0.248118001 0.23397207 0.27896785 0.23449799 0.252781687 0.215628124 0.233426813 0.27229523 0.268769194 0.2517617395 0.2368230900 0.22577370 0.263727538
SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP -0.076663968 -0.064558807 -0.093788571 -0.102411098 -0.139873649 -0.0457729741 -0.16603431 -0.066533913 -0.076129915 -0.11891191 0.19010928 -0.02884104 -0.123643922 -0.009501277 -0.002395499 -0.09928048 -0.046946835 -0.0854818844 0.0243023758 -0.05452892 -0.071302803
GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP 0.165921843 0.146439546 0.173083699 0.150887049 0.149471957 0.1345982868 0.13133671 0.153614793 0.156904617 0.14680764 0.13915461 0.18299481 0.146975954 0.155398130 0.126696824 0.15081078 0.138603009 0.1623655660 0.1023378923 0.17293499 0.129406847
>
GSVA.Rcheck/tests/test_zscore_newapi.Rout
R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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Type 'q()' to quit R.
>
> ## 2025-11-12 regression test script for method z-score
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(geneprotExpCostaEtAl2021)
>
> set.seed(2025-11-12)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 -0.1065910 0.076987224 -1.3963246 1.2771019 -0.3372823
g2 1.6144451 0.006987175 1.2139285 0.9773345 0.2874821
g3 1.3882628 -0.690659025 -2.0385616 0.2804193 -0.1822753
g4 0.7027778 0.562919910 -0.1736422 0.3117396 0.3527060
g5 2.2575002 0.199992976 -0.4118118 0.1876944 0.2664025
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> zscorePar <- zscoreParam(X, gs)
> zscore.es <- gsva(zscorePar, verbose=FALSE)
> dim(zscore.es)
[1] 100 30
> zscore.es[seq.int(min(nRowsToPrint, nrow(zscore.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 0.312867472 -1.29526532 1.33075724 1.02787224 -1.69495777 0.38374877 -0.45530090 0.6907198 -0.94561007 -0.24671418 -0.37090221 -0.79018561 -2.810724033 0.60897878 0.40967772 0.85886559 1.36114780 0.83832342 -0.03645275 0.08799549 0.796377457 0.52574294 -0.2810432 -0.8108612 0.08296071 -0.8446127 0.84867862 -0.47164723 1.0795610 -0.18999789
gs2 0.390945754 1.10418313 -0.87226678 0.98814808 0.47243587 -0.80908683 -2.02801777 -0.9519630 1.03816973 0.64288564 -0.60714603 0.78388022 1.690170005 0.08141611 -0.38821035 -0.96423057 -0.14479885 -1.63579511 2.40747184 -0.10756988 -0.771444454 -1.63609249 1.5789495 -0.8458807 -1.51847987 -0.5976987 -1.44674022 0.46805054 1.6147707 2.06394450
gs3 -0.001811199 0.77775350 -0.53571544 0.15781340 -0.78625239 1.18494771 1.40395449 0.4940425 -1.87994769 1.01593650 0.23148637 0.33298571 -0.982184346 0.50863101 0.05331591 0.21506025 -0.30401841 -0.44397530 0.98986764 0.43349581 0.367813092 -0.35414472 0.5889129 -0.6427824 -0.31534527 -1.5263270 -0.18962368 0.69729898 -1.4003458 -0.09084218
gs4 -1.591182122 0.33851802 1.72866774 -0.23472561 0.25523737 -0.43170564 0.87222298 -0.2368560 -0.04785895 0.58564428 0.13330730 0.66750172 0.564506505 0.72927044 0.67098716 -0.18260569 -0.58592420 0.75284619 1.30197620 -0.85445269 -0.557031858 -1.27899942 -1.3699200 0.7438420 -0.23199208 -1.0013757 0.73571458 -0.70703774 -0.5886431 -0.17993161
gs5 0.766796399 -0.17788043 0.64879460 -1.82069249 1.33607890 -0.63636642 0.45799028 1.6325887 -1.40583572 0.58788293 0.61646207 -1.45062352 -1.089782679 -0.54928738 -0.44923753 -1.66931867 -0.75866664 -0.92859071 -1.50660557 0.21487789 2.105102477 1.12915151 1.2298699 -0.2996151 2.15066504 0.5003593 0.95917380 -2.59290917 -0.3845605 1.38417880
gs6 -0.716279775 -0.05426807 -1.74413939 0.11786847 0.95313723 0.53717993 -1.33320625 -0.8098069 0.67096529 -1.60769629 -0.62066037 -0.95675821 2.084343406 1.05908330 -0.63258337 0.64653288 -2.19910857 0.06192974 2.09856220 1.55180093 0.048824840 -0.01453382 0.9160304 1.0380218 -0.06245326 -1.1172016 1.81550795 0.11687833 -2.0845066 0.23653569
gs7 -1.483439995 -1.61353711 0.09606499 0.18545715 0.44324489 -0.95827185 -0.53974245 1.4691095 -0.54406764 0.23311201 1.78118659 -1.03055904 -1.883717721 1.34234392 -0.60543663 -0.51247804 0.89500910 -2.68912049 0.30114473 1.71952643 -1.013116749 1.34606148 -1.0043443 0.7530808 -0.29424859 0.5523988 1.59462334 1.47630062 -0.7140522 0.69746848
gs8 0.860307942 0.12269284 -0.36366978 -0.68853630 0.25472236 -2.26226410 1.74970398 -1.4618496 1.02958245 -0.38010917 0.06612158 3.03857617 1.155055594 0.25225084 0.51153879 -0.78326508 -1.35252467 -1.52497466 -1.10486523 -0.59358348 0.211802403 -1.10327100 -0.6062342 0.4842224 1.47387664 1.1088591 -0.22975914 0.09157153 -0.6192787 0.66330053
gs9 0.472523165 -1.54177307 -1.73751327 -1.24695123 0.81431360 0.07591829 0.40272189 0.2729602 1.49697047 -0.53567505 -0.27798433 0.30741356 0.392124775 0.54653664 0.51982181 0.68185226 -0.39186260 -1.11372811 -0.24249034 -0.15242164 -0.479220486 -1.73670900 -0.8253692 0.9492306 2.58509954 1.1574484 -0.34130266 0.53725590 -0.2587282 -0.33046181
gs10 0.948714089 0.26066369 0.01517184 0.04656080 -0.41858202 0.15765701 1.60252950 -1.3415422 -1.57600572 0.85134147 -1.31980332 -0.74202025 0.008138631 -1.33037894 1.04122169 0.23937025 -0.63398866 0.40781821 -0.33280450 0.46213556 0.494260180 1.00199627 -0.0935684 1.4384559 -0.51308969 -0.6635704 -0.91780588 -0.50592456 2.6679030 -1.25485358
gs11 -1.114183957 -0.96686660 -0.85837045 1.09686667 0.66109739 0.31014287 1.54348107 0.4155154 -0.23865840 -1.31593138 -0.76585792 0.49014716 0.052378604 -0.22256842 0.42542324 -1.04723478 -0.86517479 -1.15657808 0.01218304 2.27951478 -1.030323262 -0.59593848 0.4485866 0.7385261 1.01266297 -0.1639179 -0.90215293 1.24426705 -0.6206668 1.13363125
gs12 0.140247673 0.91224938 0.19381050 0.27459303 -0.39123236 -1.52603784 0.05637403 0.3242523 2.16360821 0.59311115 0.89468052 -1.21577228 1.981331218 -0.02776069 0.48413000 0.99198020 0.55032842 0.38306471 -2.53154720 -1.22685897 0.970620849 -0.50126849 -1.2687131 -0.5789973 -0.35678825 -1.2556400 -0.13436287 -0.66596825 1.0626292 -0.29606373
gs13 0.184438429 -2.40653504 1.65236945 0.63723942 0.73915304 -0.20255853 -0.29692605 -0.1243393 0.28088936 -0.46157469 -1.43530949 0.81703811 -0.519332368 1.10096952 -1.22132641 -0.80183149 0.36806131 -0.70126108 -0.54282259 -1.12019727 1.220422842 -0.07616568 0.1338081 1.0300235 3.04657031 -0.4135226 0.92821882 -0.96999282 -0.3438475 -0.50165919
gs14 -1.915976711 -0.19142062 -0.74764472 -0.62982537 1.13589976 0.39393063 -0.99064385 -0.2339809 -0.23369031 0.53108125 -1.34294928 -0.35784509 0.265973698 -0.99179264 0.55642947 -0.89344901 0.37489191 0.53107332 0.54043848 -0.58377602 -0.691750114 0.44487165 -0.1656720 -0.5310903 2.13114853 1.7468112 -0.34695561 1.27701701 0.3804596 0.53843594
gs15 -0.818631193 0.04551576 -1.70019931 -0.24987646 0.14626427 2.27705091 0.20750749 -1.3226981 0.38056133 -0.17029152 -0.17121262 -1.57870894 -2.221533188 2.03455762 0.36889868 2.30126323 -0.26577680 0.77764716 -0.23135849 0.25343791 -0.635611331 0.02007250 -1.4961720 0.1202154 -0.33581304 0.4965537 -0.39922485 0.76546786 0.2986196 1.10347448
gs16 1.383985875 -1.60444604 0.16026385 -0.01547870 1.53953073 1.25717813 -0.79064511 -0.6283752 1.78361833 -0.02487958 -1.00102655 0.03913676 0.715561969 -1.83376784 -1.33590662 -0.91243564 -0.14861529 -0.98055913 1.27223096 -0.90182183 -1.187068456 0.50269351 -0.2710112 0.4476128 0.44634710 1.4147321 1.96002889 0.85015115 -1.0647823 -1.07225277
gs17 -0.546349412 -0.06276970 -0.61300902 -0.08782411 0.41069934 -0.09573496 2.45052706 0.3973552 0.07527670 -0.38865225 -0.61589235 0.89843549 -1.923949838 1.34341020 0.45033107 1.65005344 -0.06345493 -0.77252169 -0.86336346 0.03795593 0.535635413 -2.19248511 -0.5154797 1.6006065 -0.11560783 -0.8131597 -1.13573055 0.28030904 0.4770569 0.19833237
gs18 0.287145293 -2.00178639 1.37773397 0.28711479 -1.06272249 0.91648245 -0.90872257 0.8613990 -0.21421465 0.20877505 1.71880064 -1.28937901 0.384299786 1.69948521 -0.47855043 -0.40154009 0.65284331 -0.73495140 0.36079352 -0.18290415 0.061047045 -0.22523621 -0.4529448 0.7676323 1.34012696 -1.1920178 -1.22496138 -1.45918934 -0.4479987 1.35344006
gs19 -0.270452009 1.02911145 1.43001202 -0.22279329 -0.80248947 -1.28243504 -0.80341548 0.6234176 0.36546577 0.25597714 -0.54746138 -0.67861107 -0.224717803 -1.23724121 0.26304978 0.51214196 0.49922924 1.19277507 0.26112145 -1.14119985 -0.632479460 -0.44410671 0.3383491 -0.3900997 0.76746464 -0.3146960 0.19271387 1.83660812 -0.7595546 0.18431581
gs20 0.563927846 0.25435767 -0.51558818 0.97951789 -0.68470183 0.92458908 -0.49716214 1.5873526 -1.40358297 0.42279355 -0.03406283 -1.02108728 0.804296526 0.40209788 0.65713719 -1.33358374 -1.56853537 -0.25335622 -1.15065645 1.61164647 -1.434682219 -0.79085646 0.7585305 -0.4486147 2.34506318 0.1344800 0.01393302 -0.10523256 -0.4832695 0.26524912
gs21 -0.497382119 -0.99970708 0.51710784 -0.94363008 -0.01770256 0.89824096 1.77030151 0.6414052 -0.35718390 -0.38847464 -0.84579712 1.23036662 -0.615475860 -0.31215162 0.95791526 -0.63837032 0.84771323 -0.52788234 1.74905521 0.84206471 -1.624066701 -1.49506819 -2.1571747 0.0172747 -0.52618120 2.6954101 -0.22681844 -0.68275970 -0.2020787 0.89104992
gs22 -0.960310110 0.12232128 -0.52294604 0.14625574 2.27718580 0.15034001 -0.50698533 -0.6700677 -0.14673118 0.14856139 0.32569831 1.20144259 -0.721776120 -0.26766933 1.32557003 0.94148879 -0.21533068 -0.23873652 -0.59870256 1.02431288 -0.390839726 -0.51269518 -1.2496026 -1.5735272 -0.56091010 0.7979833 -0.19042900 -0.58318792 0.8159440 0.63334319
gs23 0.903771313 0.10707503 1.11337678 1.34028239 0.97203242 -1.09792168 -0.77494300 0.9985845 -0.39115997 -2.58228915 -0.57843401 -2.36659183 2.018157594 0.79642392 2.37997600 -0.03060408 -2.23625474 -0.54984530 -0.39947345 1.08912034 -0.355395850 -0.02409384 1.2776072 -1.2754910 0.21920764 1.3267795 -0.09384954 -0.53064055 -0.1040280 -1.15137876
gs24 1.048488767 -0.74938459 0.74945582 -0.16236564 0.64097782 -1.07837234 -1.48000793 0.4367866 1.11549132 -0.44213194 -1.32244991 0.22862740 0.604294323 -0.75489554 0.20468747 0.84933927 1.06534941 -0.66665642 2.17587243 0.41543561 -0.002039205 -0.51082038 -0.7236543 -0.1446524 -1.11671375 -0.6817531 0.03161140 0.74574871 1.6788104 -2.15507935
gs25 0.979497199 0.75832032 0.80012048 -0.85072297 1.31738300 -0.66743305 -1.61929058 1.4062036 1.48761775 1.21614430 -1.00560320 0.77157115 -0.110373306 -0.13251613 -1.11882031 0.39249026 -1.29521717 1.48372421 -1.11840120 -0.01620994 1.932263357 -0.82460250 -0.4308761 0.3284139 -0.91966370 -0.7932967 -0.84938254 -1.76875547 0.3866297 0.26078577
>
> c2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> firPar <- zscoreParam(geneExpCostaEtAl2021, c2BroadSets,
+ minSize=10, maxSize=500)
ℹ No assay name provided; using default assay 'logCPM'
> fir_es <- gsva(firPar, verbose=FALSE)
> assay(fir_es)[seq.int(min(nRowsToPrint, nrow(fir_es))),]
BS03 BS04 BS05 BS06 BS07 BS08 BS09 BS10 BS11 BS12 BS13 BS14 BS16 BS17 BS18 BS19 BS20 BS21 BS22 BS23 BS24
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP -0.0879484 -0.1115882 -0.8366884 -1.76562304 -3.69545411 1.6029629 -4.3169688 -0.41239763 -0.4961104 -2.521634699 6.78660010 0.82890187 -2.1955301 1.80221655 1.08098635 0.591597219 0.97511525 -0.24034768 1.79203134 0.7980301 0.4218498
WINTER_HYPOXIA_UP -2.5182857 -0.5300791 -2.0695142 -2.61995550 -3.59775772 1.4588409 -3.5249831 -0.85399331 -1.1974044 -2.582911963 6.58046420 1.45924220 0.2629686 4.71363501 0.62132285 0.008160728 0.15652338 -0.24228045 1.77889462 1.9483399 0.7487730
PARENT_MTOR_SIGNALING_UP -1.6981015 -1.4210951 -0.8395413 1.61629941 1.48124830 1.6737221 6.6854666 1.19964217 -1.0468539 -1.887979686 -0.27997263 0.34004171 3.8954472 -2.39197174 -5.79143532 3.219477039 -2.63457391 1.38678500 -4.01645783 -0.1097636 0.6196170
PYEON_HPV_POSITIVE_TUMORS_UP 2.7343841 1.4656636 4.0415653 -0.86118032 -2.10059613 0.8548769 0.3373314 -0.57268663 -0.7182160 1.144555625 8.70261354 6.18549711 -5.7845058 -5.55277308 0.79809178 -3.055063235 -0.66362425 -2.10868286 -0.08244479 -2.9470235 -1.8177829
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP -3.6172751 -2.8443301 -4.1573671 -2.62404284 -5.28973191 1.1595283 -4.8731844 -2.08516810 -0.7344328 -3.554794046 10.77037348 -0.52578774 -4.2542849 3.63746385 2.05322006 1.669853462 3.77913267 0.03510735 6.69480082 2.2999171 2.4610020
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP -0.7366671 1.0315930 -3.3009813 -3.16517367 -3.11784182 -3.7987337 -5.8549118 -1.69617036 -1.1788656 1.461282748 2.64067674 2.81687432 0.6279224 3.97687125 2.61068699 3.289220291 3.03570573 -1.59736596 -1.39127735 4.2035239 0.1436315
LU_TUMOR_VASCULATURE_UP 0.9325941 -0.5419310 -1.1917545 0.21817944 0.98272793 -1.0245387 0.4224972 0.74914087 -0.4249370 -0.386254019 -0.04953304 -0.23757066 0.9298349 -0.28759180 -0.50060295 1.011527831 -0.02668880 0.88408557 -1.63068594 0.8574749 -0.6859743
KORKOLA_EMBRYONAL_CARCINOMA_UP -0.4782963 -0.8695553 -0.2051284 -2.75165999 -2.12838333 1.8211865 -0.9554091 -0.70665909 -1.4180376 -0.068437844 5.25706736 1.34160873 -3.1144791 1.23217749 0.31093403 0.493955347 0.07204482 1.02097871 -0.33361404 1.8484561 -0.3687490
KORKOLA_TERATOMA_UP 0.6800061 -0.5567137 -0.4033591 -1.32007063 -0.71291217 1.0113970 -0.5004964 -0.51132115 -0.8793588 0.608720424 2.42283643 0.02983777 -0.9405311 1.22419254 -0.72840820 0.969902329 -0.31563004 1.68830010 -2.55055559 1.5371858 -0.7530217
KORKOLA_YOLK_SAC_TUMOR_UP -0.7743251 -1.2324537 -1.4228544 -1.98622450 -1.34973258 2.2122626 0.6804665 -1.81053315 -0.9045842 0.208077238 4.98573390 -0.41768595 -3.3921067 1.13221689 0.76926346 0.831830294 -0.14971540 0.79903259 0.65246016 0.8563557 0.3125163
KORKOLA_SEMINOMA_UP -1.8060155 -1.4993478 -1.7998036 -1.21611100 -0.82822646 1.7274599 0.7120294 0.38194937 -1.2922645 0.004669888 3.03489772 -0.30530984 -1.2221522 0.08284483 -0.66752455 2.506101743 0.64759843 0.62922907 -0.05312472 0.1133362 0.8497636
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP -1.3177061 -0.7251434 -1.1939368 -1.08153797 -1.82323828 1.4861036 -1.3130183 0.25088788 -1.2351018 -1.604024974 3.95689368 0.97192548 -0.8523729 1.98057224 -1.01998856 1.011538395 -0.89310164 1.95526385 0.32543686 2.3856356 -1.2650868
HOLLMAN_APOPTOSIS_VIA_CD40_UP -3.6786836 -2.6651344 -1.8497273 -1.52725352 -3.46078047 2.0554172 -2.1730543 -0.15052562 -1.2791126 -1.567296086 5.80948605 -0.60024922 -1.6636665 2.11353896 0.47083983 1.923249696 0.58574616 1.56223597 2.92058164 2.0594395 1.1149487
LIU_PROSTATE_CANCER_UP -0.8280800 -2.0343268 -1.7227901 -0.58529501 -1.66240938 2.0165928 -1.0178759 -0.54917996 -1.0931831 -0.995500188 5.69893182 0.00745604 -1.5491422 0.15647410 0.03941395 0.915970464 0.20988267 0.69151182 -0.82223852 2.2317323 0.8920552
LIU_SOX4_TARGETS_UP -1.0410303 1.5152749 -0.4995525 1.10535306 -0.78601671 -0.7351567 -3.3645890 -0.08536711 0.4678256 0.003611264 -1.01467478 1.40663055 -0.9854076 2.25422563 0.59437363 -0.083275937 -0.87160650 0.67256010 0.28262529 2.1113556 -0.9471585
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP 1.4041521 -1.4608252 -1.6122602 -0.56088419 0.33189122 1.4223219 1.2463792 0.48202350 -0.6273104 -0.134254935 3.78051741 -1.33211655 -0.2987631 -0.80724230 -3.82124613 2.080879840 -0.49164228 3.58163472 -4.41392677 -0.4681747 1.6988468
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP 0.2258399 0.8241394 -1.2072266 -0.90851041 -1.29879820 -2.4621691 -7.9493907 -1.21255762 -1.3020845 2.390675122 2.07082650 0.97473194 0.6682187 2.06208508 -1.30448581 3.121281824 0.87909816 5.18549863 -5.95621123 8.4200343 -3.2209954
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP -0.3533321 0.9308781 -0.8224510 -0.09727599 -0.07673944 1.5168423 -2.2030184 -1.23895367 0.1440840 -0.847597877 -1.22967765 1.11748428 0.6449674 0.91670336 -1.95156951 1.048898177 1.55927674 0.48748803 -0.55435439 0.5189502 0.4893975
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP -1.8061151 0.1305814 -2.4891731 0.28432747 -0.60050282 -0.9196063 -1.3846417 1.62729274 0.9518633 -0.737140462 -0.15964208 0.02823615 -0.4925713 0.64873227 1.32918331 0.315562738 1.88837006 -0.39643558 3.15429642 -0.2252624 -1.1473548
FRASOR_TAMOXIFEN_RESPONSE_UP 0.5165722 0.2865225 0.4495310 -0.33005686 -1.77264936 0.5156590 -2.1809430 -0.51654397 -0.5198969 -0.251400910 0.48247389 1.06922748 -0.4181652 0.17178745 -0.25059667 1.169931369 0.22659042 0.07487359 -0.99448884 2.4434060 -0.1718333
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP -1.7696141 0.7506279 -4.2463409 -0.49784447 -0.91318952 1.4816989 -1.3576793 0.54232743 1.2062416 -1.368498233 0.19351203 -1.33392503 0.3165982 2.39343067 -0.71971516 1.014842605 0.82292260 2.01306904 1.25572688 -0.7705576 0.9863664
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP 1.9477689 1.2663386 -0.5219991 -2.06424684 -5.91192426 -1.4560429 -9.7045731 -2.76780597 -1.2922198 -0.696265685 20.79735986 5.64457515 -9.4752524 0.72927537 4.66884657 -2.538374349 1.84287097 -1.50124329 3.45101911 1.1557712 -3.5738781
WATANABE_COLON_CANCER_MSI_VS_MSS_UP -1.0555826 -0.7709490 -0.5365729 -0.13568889 -1.56611290 1.0057152 -1.3396234 -0.92692553 -0.3886822 -0.545661596 1.23906470 1.25943523 0.5571227 -0.87912120 -0.85890546 2.185980796 0.21792505 0.15490709 0.40263300 1.3968451 0.5841967
SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP -1.3284011 -0.3758763 -2.6939462 -5.65400944 -10.40740194 2.8000397 -10.5921855 -1.81780983 -2.4305590 -7.207461540 24.17112614 3.66445033 -6.7648610 5.81586922 5.18704247 -1.944711400 1.12656890 -2.04146952 7.83194690 1.9115966 0.7500526
GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP 0.9277878 0.2661131 1.5413658 0.35386036 -0.17283152 -1.0270015 -1.5950784 -0.52242710 0.5332492 0.693567477 1.02258475 2.32773786 -1.1567629 0.26745646 -1.57158837 0.259715021 -0.70287978 1.24470508 -2.82011823 1.4624056 -1.3318606
>
> proc.time()
user system elapsed
5.643 0.215 6.060
GSVA.Rcheck/tests/test_zscore_newapi.Rout.save
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>
> ## 2025-11-12 regression test script for method z-score
>
> suppressPackageStartupMessages(library(GSVAdata))
> suppressPackageStartupMessages(library(GSVA))
>
> data(c2BroadSets)
> data(geneprotExpCostaEtAl2021)
>
> set.seed(2025-11-12)
> options(width=1024)
> nRowsToPrint <- 25
>
> p <- 10000 ## number of genes
> n <- 30 ## number of samples
> X <- matrix(rnorm(p*n), nrow=p,
+ dimnames=list(paste0("g", 1:p), paste0("s", 1:n)))
> X[1:5, 1:5]
s1 s2 s3 s4 s5
g1 -0.1065910 0.076987224 -1.3963246 1.2771019 -0.3372823
g2 1.6144451 0.006987175 1.2139285 0.9773345 0.2874821
g3 1.3882628 -0.690659025 -2.0385616 0.2804193 -0.1822753
g4 0.7027778 0.562919910 -0.1736422 0.3117396 0.3527060
g5 2.2575002 0.199992976 -0.4118118 0.1876944 0.2664025
> gs <- as.list(sample(10:100, size=100, replace=TRUE))
> gs <- lapply(gs, function(n, p)
+ paste0("g", sample(1:p, size=n, replace=FALSE)), p)
> names(gs) <- paste0("gs", 1:length(gs))
> zscorePar <- zscoreParam(X, gs)
> zscore.es <- gsva(zscorePar, verbose=FALSE)
> dim(zscore.es)
[1] 100 30
> zscore.es[seq.int(min(nRowsToPrint, nrow(zscore.es))),]
s1 s2 s3 s4 s5 s6 s7 s8 s9 s10 s11 s12 s13 s14 s15 s16 s17 s18 s19 s20 s21 s22 s23 s24 s25 s26 s27 s28 s29 s30
gs1 0.312867472 -1.29526532 1.33075724 1.02787224 -1.69495777 0.38374877 -0.45530090 0.6907198 -0.94561007 -0.24671418 -0.37090221 -0.79018561 -2.810724033 0.60897878 0.40967772 0.85886559 1.36114780 0.83832342 -0.03645275 0.08799549 0.796377457 0.52574294 -0.2810432 -0.8108612 0.08296071 -0.8446127 0.84867862 -0.47164723 1.0795610 -0.18999789
gs2 0.390945754 1.10418313 -0.87226678 0.98814808 0.47243587 -0.80908683 -2.02801777 -0.9519630 1.03816973 0.64288564 -0.60714603 0.78388022 1.690170005 0.08141611 -0.38821035 -0.96423057 -0.14479885 -1.63579511 2.40747184 -0.10756988 -0.771444454 -1.63609249 1.5789495 -0.8458807 -1.51847987 -0.5976987 -1.44674022 0.46805054 1.6147707 2.06394450
gs3 -0.001811199 0.77775350 -0.53571544 0.15781340 -0.78625239 1.18494771 1.40395449 0.4940425 -1.87994769 1.01593650 0.23148637 0.33298571 -0.982184346 0.50863101 0.05331591 0.21506025 -0.30401841 -0.44397530 0.98986764 0.43349581 0.367813092 -0.35414472 0.5889129 -0.6427824 -0.31534527 -1.5263270 -0.18962368 0.69729898 -1.4003458 -0.09084218
gs4 -1.591182122 0.33851802 1.72866774 -0.23472561 0.25523737 -0.43170564 0.87222298 -0.2368560 -0.04785895 0.58564428 0.13330730 0.66750172 0.564506505 0.72927044 0.67098716 -0.18260569 -0.58592420 0.75284619 1.30197620 -0.85445269 -0.557031858 -1.27899942 -1.3699200 0.7438420 -0.23199208 -1.0013757 0.73571458 -0.70703774 -0.5886431 -0.17993161
gs5 0.766796399 -0.17788043 0.64879460 -1.82069249 1.33607890 -0.63636642 0.45799028 1.6325887 -1.40583572 0.58788293 0.61646207 -1.45062352 -1.089782679 -0.54928738 -0.44923753 -1.66931867 -0.75866664 -0.92859071 -1.50660557 0.21487789 2.105102477 1.12915151 1.2298699 -0.2996151 2.15066504 0.5003593 0.95917380 -2.59290917 -0.3845605 1.38417880
gs6 -0.716279775 -0.05426807 -1.74413939 0.11786847 0.95313723 0.53717993 -1.33320625 -0.8098069 0.67096529 -1.60769629 -0.62066037 -0.95675821 2.084343406 1.05908330 -0.63258337 0.64653288 -2.19910857 0.06192974 2.09856220 1.55180093 0.048824840 -0.01453382 0.9160304 1.0380218 -0.06245326 -1.1172016 1.81550795 0.11687833 -2.0845066 0.23653569
gs7 -1.483439995 -1.61353711 0.09606499 0.18545715 0.44324489 -0.95827185 -0.53974245 1.4691095 -0.54406764 0.23311201 1.78118659 -1.03055904 -1.883717721 1.34234392 -0.60543663 -0.51247804 0.89500910 -2.68912049 0.30114473 1.71952643 -1.013116749 1.34606148 -1.0043443 0.7530808 -0.29424859 0.5523988 1.59462334 1.47630062 -0.7140522 0.69746848
gs8 0.860307942 0.12269284 -0.36366978 -0.68853630 0.25472236 -2.26226410 1.74970398 -1.4618496 1.02958245 -0.38010917 0.06612158 3.03857617 1.155055594 0.25225084 0.51153879 -0.78326508 -1.35252467 -1.52497466 -1.10486523 -0.59358348 0.211802403 -1.10327100 -0.6062342 0.4842224 1.47387664 1.1088591 -0.22975914 0.09157153 -0.6192787 0.66330053
gs9 0.472523165 -1.54177307 -1.73751327 -1.24695123 0.81431360 0.07591829 0.40272189 0.2729602 1.49697047 -0.53567505 -0.27798433 0.30741356 0.392124775 0.54653664 0.51982181 0.68185226 -0.39186260 -1.11372811 -0.24249034 -0.15242164 -0.479220486 -1.73670900 -0.8253692 0.9492306 2.58509954 1.1574484 -0.34130266 0.53725590 -0.2587282 -0.33046181
gs10 0.948714089 0.26066369 0.01517184 0.04656080 -0.41858202 0.15765701 1.60252950 -1.3415422 -1.57600572 0.85134147 -1.31980332 -0.74202025 0.008138631 -1.33037894 1.04122169 0.23937025 -0.63398866 0.40781821 -0.33280450 0.46213556 0.494260180 1.00199627 -0.0935684 1.4384559 -0.51308969 -0.6635704 -0.91780588 -0.50592456 2.6679030 -1.25485358
gs11 -1.114183957 -0.96686660 -0.85837045 1.09686667 0.66109739 0.31014287 1.54348107 0.4155154 -0.23865840 -1.31593138 -0.76585792 0.49014716 0.052378604 -0.22256842 0.42542324 -1.04723478 -0.86517479 -1.15657808 0.01218304 2.27951478 -1.030323262 -0.59593848 0.4485866 0.7385261 1.01266297 -0.1639179 -0.90215293 1.24426705 -0.6206668 1.13363125
gs12 0.140247673 0.91224938 0.19381050 0.27459303 -0.39123236 -1.52603784 0.05637403 0.3242523 2.16360821 0.59311115 0.89468052 -1.21577228 1.981331218 -0.02776069 0.48413000 0.99198020 0.55032842 0.38306471 -2.53154720 -1.22685897 0.970620849 -0.50126849 -1.2687131 -0.5789973 -0.35678825 -1.2556400 -0.13436287 -0.66596825 1.0626292 -0.29606373
gs13 0.184438429 -2.40653504 1.65236945 0.63723942 0.73915304 -0.20255853 -0.29692605 -0.1243393 0.28088936 -0.46157469 -1.43530949 0.81703811 -0.519332368 1.10096952 -1.22132641 -0.80183149 0.36806131 -0.70126108 -0.54282259 -1.12019727 1.220422842 -0.07616568 0.1338081 1.0300235 3.04657031 -0.4135226 0.92821882 -0.96999282 -0.3438475 -0.50165919
gs14 -1.915976711 -0.19142062 -0.74764472 -0.62982537 1.13589976 0.39393063 -0.99064385 -0.2339809 -0.23369031 0.53108125 -1.34294928 -0.35784509 0.265973698 -0.99179264 0.55642947 -0.89344901 0.37489191 0.53107332 0.54043848 -0.58377602 -0.691750114 0.44487165 -0.1656720 -0.5310903 2.13114853 1.7468112 -0.34695561 1.27701701 0.3804596 0.53843594
gs15 -0.818631193 0.04551576 -1.70019931 -0.24987646 0.14626427 2.27705091 0.20750749 -1.3226981 0.38056133 -0.17029152 -0.17121262 -1.57870894 -2.221533188 2.03455762 0.36889868 2.30126323 -0.26577680 0.77764716 -0.23135849 0.25343791 -0.635611331 0.02007250 -1.4961720 0.1202154 -0.33581304 0.4965537 -0.39922485 0.76546786 0.2986196 1.10347448
gs16 1.383985875 -1.60444604 0.16026385 -0.01547870 1.53953073 1.25717813 -0.79064511 -0.6283752 1.78361833 -0.02487958 -1.00102655 0.03913676 0.715561969 -1.83376784 -1.33590662 -0.91243564 -0.14861529 -0.98055913 1.27223096 -0.90182183 -1.187068456 0.50269351 -0.2710112 0.4476128 0.44634710 1.4147321 1.96002889 0.85015115 -1.0647823 -1.07225277
gs17 -0.546349412 -0.06276970 -0.61300902 -0.08782411 0.41069934 -0.09573496 2.45052706 0.3973552 0.07527670 -0.38865225 -0.61589235 0.89843549 -1.923949838 1.34341020 0.45033107 1.65005344 -0.06345493 -0.77252169 -0.86336346 0.03795593 0.535635413 -2.19248511 -0.5154797 1.6006065 -0.11560783 -0.8131597 -1.13573055 0.28030904 0.4770569 0.19833237
gs18 0.287145293 -2.00178639 1.37773397 0.28711479 -1.06272249 0.91648245 -0.90872257 0.8613990 -0.21421465 0.20877505 1.71880064 -1.28937901 0.384299786 1.69948521 -0.47855043 -0.40154009 0.65284331 -0.73495140 0.36079352 -0.18290415 0.061047045 -0.22523621 -0.4529448 0.7676323 1.34012696 -1.1920178 -1.22496138 -1.45918934 -0.4479987 1.35344006
gs19 -0.270452009 1.02911145 1.43001202 -0.22279329 -0.80248947 -1.28243504 -0.80341548 0.6234176 0.36546577 0.25597714 -0.54746138 -0.67861107 -0.224717803 -1.23724121 0.26304978 0.51214196 0.49922924 1.19277507 0.26112145 -1.14119985 -0.632479460 -0.44410671 0.3383491 -0.3900997 0.76746464 -0.3146960 0.19271387 1.83660812 -0.7595546 0.18431581
gs20 0.563927846 0.25435767 -0.51558818 0.97951789 -0.68470183 0.92458908 -0.49716214 1.5873526 -1.40358297 0.42279355 -0.03406283 -1.02108728 0.804296526 0.40209788 0.65713719 -1.33358374 -1.56853537 -0.25335622 -1.15065645 1.61164647 -1.434682219 -0.79085646 0.7585305 -0.4486147 2.34506318 0.1344800 0.01393302 -0.10523256 -0.4832695 0.26524912
gs21 -0.497382119 -0.99970708 0.51710784 -0.94363008 -0.01770256 0.89824096 1.77030151 0.6414052 -0.35718390 -0.38847464 -0.84579712 1.23036662 -0.615475860 -0.31215162 0.95791526 -0.63837032 0.84771323 -0.52788234 1.74905521 0.84206471 -1.624066701 -1.49506819 -2.1571747 0.0172747 -0.52618120 2.6954101 -0.22681844 -0.68275970 -0.2020787 0.89104992
gs22 -0.960310110 0.12232128 -0.52294604 0.14625574 2.27718580 0.15034001 -0.50698533 -0.6700677 -0.14673118 0.14856139 0.32569831 1.20144259 -0.721776120 -0.26766933 1.32557003 0.94148879 -0.21533068 -0.23873652 -0.59870256 1.02431288 -0.390839726 -0.51269518 -1.2496026 -1.5735272 -0.56091010 0.7979833 -0.19042900 -0.58318792 0.8159440 0.63334319
gs23 0.903771313 0.10707503 1.11337678 1.34028239 0.97203242 -1.09792168 -0.77494300 0.9985845 -0.39115997 -2.58228915 -0.57843401 -2.36659183 2.018157594 0.79642392 2.37997600 -0.03060408 -2.23625474 -0.54984530 -0.39947345 1.08912034 -0.355395850 -0.02409384 1.2776072 -1.2754910 0.21920764 1.3267795 -0.09384954 -0.53064055 -0.1040280 -1.15137876
gs24 1.048488767 -0.74938459 0.74945582 -0.16236564 0.64097782 -1.07837234 -1.48000793 0.4367866 1.11549132 -0.44213194 -1.32244991 0.22862740 0.604294323 -0.75489554 0.20468747 0.84933927 1.06534941 -0.66665642 2.17587243 0.41543561 -0.002039205 -0.51082038 -0.7236543 -0.1446524 -1.11671375 -0.6817531 0.03161140 0.74574871 1.6788104 -2.15507935
gs25 0.979497199 0.75832032 0.80012048 -0.85072297 1.31738300 -0.66743305 -1.61929058 1.4062036 1.48761775 1.21614430 -1.00560320 0.77157115 -0.110373306 -0.13251613 -1.11882031 0.39249026 -1.29521717 1.48372421 -1.11840120 -0.01620994 1.932263357 -0.82460250 -0.4308761 0.3284139 -0.91966370 -0.7932967 -0.84938254 -1.76875547 0.3866297 0.26078577
>
> c2BroadSets <- c2BroadSets[c(grep("_UP$", names(c2BroadSets)),
+ grep("_DN$", names(c2BroadSets)))]
> firPar <- zscoreParam(geneExpCostaEtAl2021, c2BroadSets,
+ minSize=10, maxSize=500)
ℹ No assay name provided; using default assay 'logCPM'
> fir_es <- gsva(firPar, verbose=FALSE)
> assay(fir_es)[seq.int(min(nRowsToPrint, nrow(fir_es))),]
BS03 BS04 BS05 BS06 BS07 BS08 BS09 BS10 BS11 BS12 BS13 BS14 BS16 BS17 BS18 BS19 BS20 BS21 BS22 BS23 BS24
WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP -0.0879484 -0.1115882 -0.8366884 -1.76562304 -3.69545411 1.6029629 -4.3169688 -0.41239763 -0.4961104 -2.521634699 6.78660010 0.82890187 -2.1955301 1.80221655 1.08098635 0.591597219 0.97511525 -0.24034768 1.79203134 0.7980301 0.4218498
WINTER_HYPOXIA_UP -2.5182857 -0.5300791 -2.0695142 -2.61995550 -3.59775772 1.4588409 -3.5249831 -0.85399331 -1.1974044 -2.582911963 6.58046420 1.45924220 0.2629686 4.71363501 0.62132285 0.008160728 0.15652338 -0.24228045 1.77889462 1.9483399 0.7487730
PARENT_MTOR_SIGNALING_UP -1.6981015 -1.4210951 -0.8395413 1.61629941 1.48124830 1.6737221 6.6854666 1.19964217 -1.0468539 -1.887979686 -0.27997263 0.34004171 3.8954472 -2.39197174 -5.79143532 3.219477039 -2.63457391 1.38678500 -4.01645783 -0.1097636 0.6196170
PYEON_HPV_POSITIVE_TUMORS_UP 2.7343841 1.4656636 4.0415653 -0.86118032 -2.10059613 0.8548769 0.3373314 -0.57268663 -0.7182160 1.144555625 8.70261354 6.18549711 -5.7845058 -5.55277308 0.79809178 -3.055063235 -0.66362425 -2.10868286 -0.08244479 -2.9470235 -1.8177829
NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP -3.6172751 -2.8443301 -4.1573671 -2.62404284 -5.28973191 1.1595283 -4.8731844 -2.08516810 -0.7344328 -3.554794046 10.77037348 -0.52578774 -4.2542849 3.63746385 2.05322006 1.669853462 3.77913267 0.03510735 6.69480082 2.2999171 2.4610020
PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP -0.7366671 1.0315930 -3.3009813 -3.16517367 -3.11784182 -3.7987337 -5.8549118 -1.69617036 -1.1788656 1.461282748 2.64067674 2.81687432 0.6279224 3.97687125 2.61068699 3.289220291 3.03570573 -1.59736596 -1.39127735 4.2035239 0.1436315
LU_TUMOR_VASCULATURE_UP 0.9325941 -0.5419310 -1.1917545 0.21817944 0.98272793 -1.0245387 0.4224972 0.74914087 -0.4249370 -0.386254019 -0.04953304 -0.23757066 0.9298349 -0.28759180 -0.50060295 1.011527831 -0.02668880 0.88408557 -1.63068594 0.8574749 -0.6859743
KORKOLA_EMBRYONAL_CARCINOMA_UP -0.4782963 -0.8695553 -0.2051284 -2.75165999 -2.12838333 1.8211865 -0.9554091 -0.70665909 -1.4180376 -0.068437844 5.25706736 1.34160873 -3.1144791 1.23217749 0.31093403 0.493955347 0.07204482 1.02097871 -0.33361404 1.8484561 -0.3687490
KORKOLA_TERATOMA_UP 0.6800061 -0.5567137 -0.4033591 -1.32007063 -0.71291217 1.0113970 -0.5004964 -0.51132115 -0.8793588 0.608720424 2.42283643 0.02983777 -0.9405311 1.22419254 -0.72840820 0.969902329 -0.31563004 1.68830010 -2.55055559 1.5371858 -0.7530217
KORKOLA_YOLK_SAC_TUMOR_UP -0.7743251 -1.2324537 -1.4228544 -1.98622450 -1.34973258 2.2122626 0.6804665 -1.81053315 -0.9045842 0.208077238 4.98573390 -0.41768595 -3.3921067 1.13221689 0.76926346 0.831830294 -0.14971540 0.79903259 0.65246016 0.8563557 0.3125163
KORKOLA_SEMINOMA_UP -1.8060155 -1.4993478 -1.7998036 -1.21611100 -0.82822646 1.7274599 0.7120294 0.38194937 -1.2922645 0.004669888 3.03489772 -0.30530984 -1.2221522 0.08284483 -0.66752455 2.506101743 0.64759843 0.62922907 -0.05312472 0.1133362 0.8497636
WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP -1.3177061 -0.7251434 -1.1939368 -1.08153797 -1.82323828 1.4861036 -1.3130183 0.25088788 -1.2351018 -1.604024974 3.95689368 0.97192548 -0.8523729 1.98057224 -1.01998856 1.011538395 -0.89310164 1.95526385 0.32543686 2.3856356 -1.2650868
HOLLMAN_APOPTOSIS_VIA_CD40_UP -3.6786836 -2.6651344 -1.8497273 -1.52725352 -3.46078047 2.0554172 -2.1730543 -0.15052562 -1.2791126 -1.567296086 5.80948605 -0.60024922 -1.6636665 2.11353896 0.47083983 1.923249696 0.58574616 1.56223597 2.92058164 2.0594395 1.1149487
LIU_PROSTATE_CANCER_UP -0.8280800 -2.0343268 -1.7227901 -0.58529501 -1.66240938 2.0165928 -1.0178759 -0.54917996 -1.0931831 -0.995500188 5.69893182 0.00745604 -1.5491422 0.15647410 0.03941395 0.915970464 0.20988267 0.69151182 -0.82223852 2.2317323 0.8920552
LIU_SOX4_TARGETS_UP -1.0410303 1.5152749 -0.4995525 1.10535306 -0.78601671 -0.7351567 -3.3645890 -0.08536711 0.4678256 0.003611264 -1.01467478 1.40663055 -0.9854076 2.25422563 0.59437363 -0.083275937 -0.87160650 0.67256010 0.28262529 2.1113556 -0.9471585
BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP 1.4041521 -1.4608252 -1.6122602 -0.56088419 0.33189122 1.4223219 1.2463792 0.48202350 -0.6273104 -0.134254935 3.78051741 -1.33211655 -0.2987631 -0.80724230 -3.82124613 2.080879840 -0.49164228 3.58163472 -4.41392677 -0.4681747 1.6988468
SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP 0.2258399 0.8241394 -1.2072266 -0.90851041 -1.29879820 -2.4621691 -7.9493907 -1.21255762 -1.3020845 2.390675122 2.07082650 0.97473194 0.6682187 2.06208508 -1.30448581 3.121281824 0.87909816 5.18549863 -5.95621123 8.4200343 -3.2209954
DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP -0.3533321 0.9308781 -0.8224510 -0.09727599 -0.07673944 1.5168423 -2.2030184 -1.23895367 0.1440840 -0.847597877 -1.22967765 1.11748428 0.6449674 0.91670336 -1.95156951 1.048898177 1.55927674 0.48748803 -0.55435439 0.5189502 0.4893975
FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP -1.8061151 0.1305814 -2.4891731 0.28432747 -0.60050282 -0.9196063 -1.3846417 1.62729274 0.9518633 -0.737140462 -0.15964208 0.02823615 -0.4925713 0.64873227 1.32918331 0.315562738 1.88837006 -0.39643558 3.15429642 -0.2252624 -1.1473548
FRASOR_TAMOXIFEN_RESPONSE_UP 0.5165722 0.2865225 0.4495310 -0.33005686 -1.77264936 0.5156590 -2.1809430 -0.51654397 -0.5198969 -0.251400910 0.48247389 1.06922748 -0.4181652 0.17178745 -0.25059667 1.169931369 0.22659042 0.07487359 -0.99448884 2.4434060 -0.1718333
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP -1.7696141 0.7506279 -4.2463409 -0.49784447 -0.91318952 1.4816989 -1.3576793 0.54232743 1.2062416 -1.368498233 0.19351203 -1.33392503 0.3165982 2.39343067 -0.71971516 1.014842605 0.82292260 2.01306904 1.25572688 -0.7705576 0.9863664
SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP 1.9477689 1.2663386 -0.5219991 -2.06424684 -5.91192426 -1.4560429 -9.7045731 -2.76780597 -1.2922198 -0.696265685 20.79735986 5.64457515 -9.4752524 0.72927537 4.66884657 -2.538374349 1.84287097 -1.50124329 3.45101911 1.1557712 -3.5738781
WATANABE_COLON_CANCER_MSI_VS_MSS_UP -1.0555826 -0.7709490 -0.5365729 -0.13568889 -1.56611290 1.0057152 -1.3396234 -0.92692553 -0.3886822 -0.545661596 1.23906470 1.25943523 0.5571227 -0.87912120 -0.85890546 2.185980796 0.21792505 0.15490709 0.40263300 1.3968451 0.5841967
SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP -1.3284011 -0.3758763 -2.6939462 -5.65400944 -10.40740194 2.8000397 -10.5921855 -1.81780983 -2.4305590 -7.207461540 24.17112614 3.66445033 -6.7648610 5.81586922 5.18704247 -1.944711400 1.12656890 -2.04146952 7.83194690 1.9115966 0.7500526
GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP 0.9277878 0.2661131 1.5413658 0.35386036 -0.17283152 -1.0270015 -1.5950784 -0.52242710 0.5332492 0.693567477 1.02258475 2.32773786 -1.1567629 0.26745646 -1.57158837 0.259715021 -0.70287978 1.24470508 -2.82011823 1.4624056 -1.3318606
>
GSVA.Rcheck/GSVA-Ex.timings
| name | user | system | elapsed | |
| computeGeneSetsOverlap | 0.019 | 0.000 | 0.024 | |
| filterGeneSets | 0.000 | 0.001 | 0.000 | |
| gsva | 0.121 | 0.008 | 0.149 | |
| gsvaEnrichment | 0.033 | 0.003 | 0.039 | |
| gsvaParam-class | 0.443 | 0.018 | 0.501 | |
| gsvaRanks | 0.068 | 0.002 | 0.072 | |
| igsva | 0 | 0 | 0 | |
| plageParam-class | 0.384 | 0.014 | 0.426 | |
| readGMT | 0.205 | 0.011 | 0.228 | |
| ssgseaParam-class | 0.401 | 0.013 | 0.458 | |
| zscoreParam-class | 0.409 | 0.013 | 0.438 | |