Galfrè Silvia Giulia
| Snapshot Date: 2025-10-03 13:45 -0400 (Fri, 03 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/COTAN |
| git_branch: devel |
| git_last_commit: 260f3bf |
| git_last_commit_date: 2025-09-26 15:15:57 -0400 (Fri, 26 Sep 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-04 12:03 -0400 (Sat, 04 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4853 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4640 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4585 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4576 |
| 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 455/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| COTAN 2.9.6 (landing page) Galfrè Silvia Giulia
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the COTAN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COTAN.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: COTAN |
| Version: 2.9.6 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings COTAN_2.9.6.tar.gz |
| StartedAt: 2025-10-03 22:34:47 -0400 (Fri, 03 Oct 2025) |
| EndedAt: 2025-10-03 23:08:01 -0400 (Fri, 03 Oct 2025) |
| EllapsedTime: 1994.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: COTAN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings COTAN_2.9.6.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/COTAN.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘2.9.6’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘COTAN’ can be installed ... OK
* 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 loading without being on the library search path ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
UniformClusters 2189.895 6.134 161.828
CalculatingCOEX 1294.958 2.374 91.824
HeatmapPlots 884.324 0.934 47.502
COTAN_ObjectCreation 360.246 0.703 22.139
HandlingClusterizations 339.088 0.847 47.387
GenesStatistics 304.618 0.980 16.014
ParametersEstimations 25.376 0.302 23.873
Conversions 5.060 0.076 5.136
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘outputTestDatasetCreation.R’
Running ‘spelling.R’
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘COTAN’ ... ** this is package ‘COTAN’ version ‘2.9.6’ ** using staged installation ** R ** data ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (COTAN)
COTAN.Rcheck/tests/outputTestDatasetCreation.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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.
>
> # Creates the files to be reloaded by the tests for comparisons
>
> outputTestDatasetCreation <-
+ function(testsDir = file.path("tests", "testthat")) {
+ utils::data("test.dataset", package = "COTAN")
+ options(parallelly.fork.enable = TRUE)
+ setLoggingLevel(3L)
+
+ obj <- COTAN(raw = test.dataset)
+ obj <- initializeMetaDataset(objCOTAN = obj, GEO = " ",
+ sequencingMethod = "artificial",
+ sampleCondition = "test")
+
+ obj <- proceedToCoex(objCOTAN = obj, cores = 6L, saveObj = FALSE)
+
+ if (FALSE) {
+ saveRDS(obj, file = file.path(testsDir,"test.COTAN.RDS"))
+ }
+
+ cells.names.test <- getCells(objCOTAN = obj)[c(1L:10L, 591L:610L, 991L:1000L)]
+ genes.names.test <- getGenes(objCOTAN = obj)[c(1L:10L, 291L:310L, 591L: 600L)]
+ saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS"))
+ saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS"))
+
+ pcaRaw <- runPCA(x = getRawData(objCOTAN = obj), rank = 10L,
+ BSPARAM = IrlbaParam(), get.rotation = FALSE)[["x"]]
+
+ pca.raw.test <- pcaRaw[genes.names.test, ]
+ saveRDS(pca.raw.test, file.path(testsDir, "pca.raw.test.RDS"))
+
+ dispersion.test <- getDispersion(objCOTAN = obj)[genes.names.test]
+ saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS"))
+
+ raw.norm.test <-
+ getNuNormData(objCOTAN = obj)[genes.names.test, cells.names.test]
+ saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS"))
+
+ coex.test <-
+ getGenesCoex(objCOTAN = obj, genes = genes.names.test, zeroDiagonal = FALSE)
+ saveRDS(coex.test, file.path(testsDir, "coex.test.RDS"))
+
+ lambda.test <- getLambda(objCOTAN = obj)[genes.names.test]
+ saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS"))
+
+ GDI.test <- calculateGDI(objCOTAN = obj)
+ GDI.test <- GDI.test[genes.names.test, ]
+ saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS"))
+
+ nu.test <- getNu(objCOTAN = obj)[cells.names.test]
+ saveRDS(nu.test, file.path(testsDir, "nu.test.RDS"))
+
+ pvalues.test <- calculatePValue(objCOTAN = obj,
+ geneSubsetCol = genes.names.test,
+ geneSubsetRow = genes.names.test)
+ saveRDS(pvalues.test, file.path(testsDir, "pvalues.test.RDS"))
+
+ groupMarkers <- list(G1 = c("g-000010", "g-000020", "g-000030"),
+ G2 = c("g-000300", "g-000330", "g-000660"),
+ G3 = c("g-000510", "g-000530", "g-000550",
+ "g-000570", "g-000590"))
+
+ gcsData <- genesCoexSpace(objCOTAN = obj,
+ primaryMarkers = unlist(groupMarkers),
+ numGenesPerMarker = 11L)
+
+ genes.coex.space.test <- gcsData[["GCS"]]
+ saveRDS(genes.coex.space.test,
+ file.path(testsDir, "genes.coex.space.test.RDS"))
+
+ genesClustersData <-
+ establishGenesClusters(objCOTAN = obj,
+ groupMarkers = groupMarkers,
+ numGenesPerMarker = 11L,
+ kCuts = 6L, distance = "cosine",
+ hclustMethod = "ward.D2")
+
+ pca.genes.clusters.test <- genesClustersData[["pca_clusters"]]
+ saveRDS(pca.genes.clusters.test,
+ file.path(testsDir, "pca.genes.clusters.test.RDS"))
+
+ # Make it a less strict check as it is only for testing
+ checker <- new("AdvancedGDIUniformityCheck")
+ checker <- shiftCheckerThresholds(checker, 0.1)
+
+ initialResolution <- 0.8
+ splitData <- cellsUniformClustering(objCOTAN = obj,
+ checker = checker,
+ initialResolution = initialResolution,
+ useCoexEigen = TRUE,
+ dataMethod = "LL",
+ numReducedComp = 50L,
+ cores = 6L, optimizeForSpeed = TRUE,
+ deviceStr = "cuda", saveObj = FALSE)
+
+ split.clusters.test <- splitData[["clusters"]]
+ saveRDS(split.clusters.test, file.path(testsDir, "split.clusters.test.RDS"))
+
+ obj <- addClusterization(objCOTAN = obj,
+ clName = "split",
+ clusters = splitData[["clusters"]],
+ coexDF = splitData[["coex"]])
+
+ coex.clusters.test <- splitData[["coex"]][genes.names.test, ]
+ saveRDS(coex.clusters.test, file.path(testsDir, "coex.clusters.test.RDS"))
+
+ pvalDF <- pValueFromDEA(splitData[["coex"]],
+ getNumCells(objCOTAN = obj),
+ adjustmentMethod = "none")
+
+ pvalues.clusters.test <- pvalDF[genes.names.test, ]
+ saveRDS(pvalues.clusters.test,
+ file.path(testsDir, "pvalues.clusters.test.RDS"))
+
+ mergedData <- mergeUniformCellsClusters(objCOTAN = obj,
+ clusters = splitData[["clusters"]],
+ checkers = checker,
+ cores = 6L,
+ distance = "cosine",
+ hclustMethod = "ward.D2",
+ saveObj = FALSE)
+
+ merge.clusters.test <- mergedData[["clusters"]]
+ saveRDS(merge.clusters.test, file.path(testsDir, "merge.clusters.test.RDS"))
+
+ obj <- addClusterization(objCOTAN = obj,
+ clName = "merge",
+ clusters = mergedData[["clusters"]],
+ coexDF = mergedData[["coex"]])
+ }
>
> proc.time()
user system elapsed
0.155 0.037 0.181
COTAN.Rcheck/tests/spelling.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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.
> if (requireNamespace("spelling", quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
All Done!
>
> proc.time()
user system elapsed
0.134 0.041 0.164
COTAN.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
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.
> Sys.setenv(R_TESTS = "")
> library(testthat)
> library(COTAN)
> library(zeallot)
> test_check("COTAN")
Setting new log level to 4
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.90998482704163
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 4.00851607322693
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000628471374511719
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00724172592163086
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.13541102409363
Total calculations elapsed time: 5.1517972946167
Calculate genes' COEX (legacy): DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 5 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 4 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 6.27560210227966
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 7 cells batches
Total calculations elapsed time: 1.08622860908508
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75595238095238 | median: 1.07156808035714 | mean: 1.07156808035714
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.5687997341156
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03734183779544 | max: 4.61112297272667 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.785312652587891
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0295487661210321 | median: 0.016072261901129 | mean: 0.016072261901129
`nu` mean: 1.69786080481514
Marginal errors | max: 1.95799528048 | median 1.32268477389029 | mean: 1.33563364783916
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.64519715309143
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.0585450475968788 | max: 3.52739274166646 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.797682046890259
Estimate `nu`: DONE
`nu` change (abs) | max: 0.417150556912302 | median: 0.240156504520849 | mean: 0.240156504520849
`nu` mean: 0.823005947608547
Marginal errors | max: 0.837672524335753 | median 0.704691669139061 | mean: 0.646575831699995
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.61029815673828
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.328845855849147 | max: 4.03031691940854 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.826888799667358
Estimate `nu`: DONE
`nu` change (abs) | max: 0.164439840041 | median: 0.0957105992188852 | mean: 0.0957105992188852
`nu` mean: 1.06872924082212
Marginal errors | max: 0.260109847946692 | median 0.21392791155499 | mean: 0.197565106613055
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.50445628166199
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.229469002841045 | max: 3.87206403670079 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.745267152786255
Estimate `nu`: DONE
`nu` change (abs) | max: 0.05539667181205 | median: 0.0321044921874999 | mean: 0.0321044921874999
`nu` mean: 0.97670782037545
Marginal errors | max: 0.095347789718808 | median 0.0796003827042702 | mean: 0.0725509735761708
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.56611323356628
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.263830434255107 | max: 3.92953043775907 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.755551099777222
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0196209299693411 | median: 0.0114037947200925 | mean: 0.0114037947200925
`nu` mean: 1.00821713524925
Marginal errors | max: 0.0329495161656741 | median 0.0273479725376324 | mean: 0.0250296751521303
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.51427555084229
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.251734659898779 | max: 3.9096133246649 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.745208978652954
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0069104540740097 | median: 0.0040109538496062 | mean: 0.0040109538496062
`nu` mean: 0.997100499775596
Marginal errors | max: 0.0116950057438405 | median 0.00972280144873849 | mean: 0.00889105008777538
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.51420378684998
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.256009779031907 | max: 3.91667271750655 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.697680711746216
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00251004753849005 | median: 0.00146484374999994 | mean: 0.00146484374999994
`nu` mean: 1.00104520378849
Marginal errors | max: 0.00430755646112857 | median 0.00358203399504298 | mean: 0.00327684342604044
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.50657629966736
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.254429717857093 | max: 3.91406908073254 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.724236726760864
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00104629156456748 | median: 0.000592910406456731 | mean: 0.000592910406456731
`nu` mean: 0.999546618841889
Marginal errors | max: 0.00162038706091039 | median 0.00134441676098973 | mean: 0.00123030512553246
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.48929286003113
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.255022049769696 | max: 3.91504587939868 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.782500743865967
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000418450901304768 | median: 0.000244140625000028 | mean: 0.000244140625000028
`nu` mean: 1.0001743102763
Marginal errors | max: 0.00071569233034019 | median 0.000597297218559056 | mean: 0.000545906995078305
Total calculations elapsed time: 41.9697525501251
Estimate `dispersion`/`nu`: DONE
Estimate `dispersion`/`nu`: START
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.45501518249512
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.59300446510315
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000643730163574219
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00294184684753418
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.813565969467163
Total calculations elapsed time: 3.41015601158142
Calculate genes' COEX (legacy): DONE
Calculate cells' COEX (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 2.71927881240845
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000684499740600586
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.0020744800567627
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.953728199005127
Total calculations elapsed time: 3.67576599121094
Calculate cells' COEX (legacy): DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0093836784362793
Calculate `GDI`: DONE
Total calculations elapsed time: 2.47395253181458
Calculate GDI dataframe: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00359964370727539
Calculate `GDI`: DONE
Total calculations elapsed time: 2.53595757484436
Calculate GDI dataframe: DONE
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Selected 5 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 5 genes using HVG_Seurat selector
Running genes' selection: DONE
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer data
Calculating gene means
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating gene variance to mean ratios
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Running genes' selection: START
Given 5 genes as input
Running genes' selection: DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 1.62337851524353
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 1.63120627403259
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Selected 8 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 1.71969819068909
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Normalizing layer: counts
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Selected 8 genes using HVG_Seurat selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 2.57354950904846
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 2.3993079662323
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 2.32893371582031
Elaborating Reduced dimensionality Data Matrix - DONE
Initializing `COTAN` meta-data
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.61319518089294
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.796880722045898
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 1.735699617106 | median 1.3799744133366 | mean: 1.32181397451301
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.5343325138092
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.0655494303592343 | max: 3.54400580804152 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.73483681678772
Estimate `nu`: DONE
`nu` change (abs) | max: 0.402649984216273 | median: 0.231868788425666 | mean: 0.231868788425666
`nu` mean: 0.829218804209393
Marginal errors | max: 0.803248939260364 | median 0.677504196374578 | mean: 0.619386446933353
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.47661757469177
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.326019058449519 | max: 4.02612397202046 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.741996765136719
Estimate `nu`: DONE
`nu` change (abs) | max: 0.158004893526231 | median: 0.0919692884670312 | mean: 0.0919692884670312
`nu` mean: 1.0660356050592
Marginal errors | max: 0.250677002875358 | median 0.206241644985115 | mean: 0.190402167377957
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.56780242919922
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.230397316576369 | max: 3.87365659194104 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.798199653625488
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0532774732102337 | median: 0.0308837890624999 | mean: 0.0308837890624999
`nu` mean: 0.977606315852266
Marginal errors | max: 0.0916920322976189 | median 0.0765360853958157 | mean: 0.0697673030094073
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.49811005592346
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.263457616228195 | max: 3.928924407347 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.763133525848389
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0187878665732679 | median: 0.0109155550210726 | mean: 0.0109155550210726
`nu` mean: 1.0078723115522
Marginal errors | max: 0.0315207323253404 | median 0.0261635598193228 | mean: 0.0239435763640454
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.55319309234619
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.251890641847533 | max: 3.90987172241566 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.73970627784729
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00649137083358098 | median: 0.00376680890457393 | mean: 0.00376680890457393
`nu` mean: 0.997275438070993
Marginal errors | max: 0.0109748802265024 | median 0.00912386940474885 | mean: 0.00834350038184262
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.58444976806641
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.255902752363649 | max: 3.91649655995187 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.762251377105713
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00230094227000666 | median: 0.00132529141000018 | mean: 0.00132529141000018
`nu` mean: 1.00097565086001
Marginal errors | max: 0.00376864912836616 | median 0.00313421412286008 | mean: 0.00286709489297543
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.52036833763123
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.254520292119112 | max: 3.91421850264948 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.765236854553223
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000837013154366462 | median: 0.000488281250000028 | mean: 0.000488281250000028
`nu` mean: 0.999651268095634
Marginal errors | max: 0.00144055320514802 | median 0.00119489364392944 | mean: 0.00109355439757213
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.54940581321716
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.255046800817986 | max: 3.9150866760965 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.807352066040039
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000418448154490214 | median: 0.000244140624999917 | mean: 0.000244140624999917
`nu` mean: 1.00017430752949
Marginal errors | max: 0.000715683388516908 | median 0.000597284734240588 | mean: 0.000545899916524029
Total calculations elapsed time: 41.7506060600281
Estimate `dispersion`/`nu`: DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.499924659729
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000501155853271484
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0013425350189209
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.803682327270508
Total calculations elapsed time: 3.3054506778717
Calculate genes' COEX (legacy): DONE
Calculate cells' COEX (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 2.68139815330505
Calculating cells' COEX normalization factor
Calculate cells' normalization factor elapsed time: 0.000519275665283203
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00140070915222168
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.888674736022949
Total calculations elapsed time: 3.57199287414551
Calculate cells' COEX (legacy): DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00307345390319824
Calculate `GDI`: DONE
Total calculations elapsed time: 2.71026468276978
Calculate GDI dataframe: DONE
Calculate genes' partial COEX: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0.325
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial COEX
Total calculations elapsed time: 7.09428238868713
Calculate genes' partial COEX: DONE
Calculate cells' partial COEX: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial COEX
Total calculations elapsed time: 6.45479941368103
Calculate cells' partial COEX: DONE
Asked to drop 2 genes and 0 cells
Asked to drop 0 genes and 4 cells
Asked to drop 2 genes and 2 cells
Attaching package: 'rlang'
The following objects are masked from 'package:testthat':
is_false, is_null, is_true
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
calculating YY.. done
calculating YY.. done
calculating YN..NY..NN..t().. done
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.170325756073
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
calculating NN.. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.64825391769409
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000710964202880859
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00143074989318848
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.800184726715088
Total calculations elapsed time: 3.45058035850525
Calculate genes' COEX (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.63404870033264
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000515937805175781
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00134181976318359
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.8378005027771
Total calculations elapsed time: 3.4737069606781
Calculate genes' COEX (legacy): DONE
Calculate genes' partial COEX: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0.1
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial COEX
Total calculations elapsed time: 6.34901666641235
Calculate genes' partial COEX: DONE
Calculate genes' partial COEX: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0.4
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial COEX
Total calculations elapsed time: 6.61964106559753
Calculate genes' partial COEX: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
calculating YY.. done
calculating YY.. done
calculating NY..YN..NN..t().. done
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.21037602424622
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.794437646865845
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 0.255290533439036 | median 0.080731376500534 | mean: 0.101968565509111
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.31217622756958
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03709166563768 | max: 4.61069655774133 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.780734300613403
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00330148418741771 | median 0.00111713187082163 | mean: 0.00132007186543017
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.27297306060791
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03887279473672 | max: 4.60974134092906 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.796177387237549
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median: 0 | mean: 0
`nu` mean: 1.69735147626627
Marginal errors | max: 5.14174422185931e-05 | median 1.68182247684001e-07 | mean: 5.57649710817287e-06
Total calculations elapsed time: 19.4855163097382
Estimate `dispersion`/`nu`: DONE
calculating NN.. done
calculating NN.. done
calculating YN..NY..YY..t().. done
Calculate cells' COEX (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 3.43436169624329
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000792264938354492
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.0016937255859375
Estimating cells' COEX
Calculate cells' COEX elapsed time: 1.17110157012939
Total calculations elapsed time: 4.60794925689697
Calculate cells' COEX (legacy): DONE
Calculate cells' partial COEX: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial COEX
Total calculations elapsed time: 7.04145503044128
Calculate cells' partial COEX: DONE
Calculate cells' partial COEX: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial COEX normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial COEX
Total calculations elapsed time: 6.71901631355286
Calculate cells' partial COEX: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.40044569969177
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.841622114181519
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 0.255290533439036 | median 0.080731376500534 | mean: 0.101968565509111
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.30214214324951
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03709166563768 | max: 4.61069655774133 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.807534694671631
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00330148418741771 | median 0.00111713187082163 | mean: 0.00132007186543017
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.6230320930481
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03887279473672 | max: 4.60974134092906 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.86020827293396
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median: 0 | mean: 0
`nu` mean: 1.69735147626627
Marginal errors | max: 5.14174422185931e-05 | median 1.68182247684001e-07 | mean: 5.57649710817287e-06
Total calculations elapsed time: 20.4722402095795
Estimate `dispersion`/`nu`: DONE
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.80073237419128
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000519990921020508
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0013420581817627
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.814330339431763
Total calculations elapsed time: 3.61692476272583
Calculate genes' COEX (legacy): DONE
Calculating S: START
Calculating S: DONE
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Total calculations elapsed time: 6.11165380477905
Calculating G: DONE
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values genome wide on columns and genome wide on rows
Total calculations elapsed time: 0.00234484672546387
calculating PValues: DONE
Using G
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Total calculations elapsed time: 6.42431044578552
Calculating G: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
Total calculations elapsed time: 6.42559432983398
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00325298309326172
Calculate `GDI`: DONE
Total calculations elapsed time: 2.53320980072021
Calculate GDI dataframe: DONE
Calculate GDI dataframe: START
Using G
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Total calculations elapsed time: 6.45456767082214
Calculating G: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00322151184082031
Calculate `GDI`: DONE
Total calculations elapsed time: 9.0031099319458
Calculate GDI dataframe: DONE
Calculate `GDI`: START
Calculating S: START
Calculating S: DONE
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00470399856567383
Calculate `GDI`: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00383830070495605
Calculate `GDI`: DONE
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 0.921923637390137
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.01304793357849
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 2.97253561019897
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 8.91037940979004
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00678682327270508
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0517933368682861
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.07586312294006
Total calculations elapsed time: 10.0448226928711
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 11.051185131073
Dataset analysis elapsed time: 14.9456443786621
COTAN dataset analysis: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 1.01333093643188
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.27827000617981
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 3.31028056144714
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 9.20820140838623
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00631880760192871
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0514159202575684
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.875017404556274
Total calculations elapsed time: 10.140953540802
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 10.9946403503418
Dataset analysis elapsed time: 15.3182518482208
COTAN dataset analysis: DONE
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
Total calculations elapsed time: 0.0235693454742432
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0408134460449219
Calculate `GDI`: DONE
Total calculations elapsed time: 2.69275879859924
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 0.851996660232544
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 1.82984018325806
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 2.6526620388031
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 8.65827226638794
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00711584091186523
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0525920391082764
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.838683128356934
Total calculations elapsed time: 9.55666327476501
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 10.4196877479553
Dataset analysis elapsed time: 13.924346446991
COTAN dataset analysis: DONE
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
Total calculations elapsed time: 0.018352746963501
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.033963680267334
Calculate `GDI`: DONE
Total calculations elapsed time: 2.51333045959473
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 0.895862102508545
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 1.91667866706848
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 2.7667191028595
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 8.72016978263855
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00724267959594727
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0505416393280029
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.854374408721924
Total calculations elapsed time: 9.63232851028442
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 10.4720633029938
Dataset analysis elapsed time: 14.1346445083618
COTAN dataset analysis: DONE
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
Total calculations elapsed time: 0.0081329345703125
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0339250564575195
Calculate `GDI`: DONE
Total calculations elapsed time: 2.60432934761047
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Asked to drop 0 genes and 1160 cells
COTAN dataset analysis: START
Asked to drop 31 genes and 0 cells
Genes/cells selection done: dropped [31] genes and [0] cells
Working on [569] genes and [40] cells
Dataset cleaning elapsed time: 0.89116644859314
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 6 iterations
Total calculations elapsed time: 1.56798958778381
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.212044752677142 | max: 85.4528331044018 | % negative: 62.2144112478032
Model parameter estimation elapsed time: 2.36824345588684
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.85419750213623
Dataset analysis elapsed time: 4.11360740661621
COTAN dataset analysis: DONE
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 8.18713116645813
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00564336776733398
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00821566581726074
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.914398193359375
Total calculations elapsed time: 9.1153883934021
Calculate genes' COEX (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 8.05943465232849
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00631833076477051
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00841379165649414
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.897974491119385
Total calculations elapsed time: 8.97214126586914
Calculate genes' COEX (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 8.57733631134033
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00724244117736816
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0090935230255127
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.879866600036621
Total calculations elapsed time: 9.47353887557983
Calculate genes' COEX (legacy): DONE
Hangling COTAN object with condition: test
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
Total calculations elapsed time: 0.00493311882019043
calculating PValues: DONE
Handling genes type: G2
Handling genes type: G3
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Clean plots: START
PCA: START
PCA: DONE
Hierarchical clustering: START
Hierarchical clustering: DONE
Total calculations elapsed time: 2.0360426902771
Clean plots: DONE
Dataset cleaning elapsed time: 4.21280097961426
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 1.97084069252014
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 2.83822894096375
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 9.13468337059021
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00529885292053223
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0533683300018311
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.898563861846924
Total calculations elapsed time: 10.0919144153595
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 10.9946191310883
Dataset analysis elapsed time: 18.0456490516663
COTAN dataset analysis: DONE
Saving elaborated data locally at: /tmp/Rtmp1jq8Pz/test.cotan.RDS
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 2.94123148918152
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 41850
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5751
Number of communities: 2
Elapsed time: 0 seconds
Number of clusters is too small. Reclustering at resolution higher than: 0.8
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 41850
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.3786
Number of communities: 7
Elapsed time: 0 seconds
2 singletons identified. 5 final clusters.
Used resolution for Seurat clusterization is: 1.3
Total calculations elapsed time: 4.10493993759155
Creating new clusterization: DONE
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Asked to drop no genes or cells
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 3.180006980896
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 29356
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5763
Number of communities: 2
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
Total calculations elapsed time: 4.05651450157166
Creating new clusterization: DONE
Creating PDF UMAP in file: /tmp/Rtmp1jq8Pz/test/reclustering/pdf_umap_1.pdf
UMAP plot: START
Calculating UMAP: START
22:55:20 UMAP embedding parameters a = 0.9922 b = 1.112
22:55:20 Read 1200 rows and found 65 numeric columns
22:55:20 Using Annoy for neighbor search, n_neighbors = 30
22:55:20 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:55:20 Writing NN index file to temp file /tmp/Rtmp1jq8Pz/file341eb927f03061
22:55:20 Searching Annoy index using 1 thread, search_k = 3000
22:55:21 Annoy recall = 100%
22:55:22 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:55:24 Initializing from normalized Laplacian + noise (using RSpectra)
22:55:24 Commencing optimization for 500 epochs, with 48472 positive edges
22:55:24 Using rng type: pcg
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:55:26 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.88180994987488
UMAP plot: DONE
UMAP plot: START
Calculating UMAP: START
22:55:26 UMAP embedding parameters a = 0.9922 b = 1.112
22:55:26 Read 1200 rows and found 65 numeric columns
22:55:26 Using Annoy for neighbor search, n_neighbors = 30
22:55:26 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:55:27 Writing NN index file to temp file /tmp/Rtmp1jq8Pz/file341eb9145d47a3
22:55:27 Searching Annoy index using 1 thread, search_k = 3000
22:55:27 Annoy recall = 100%
22:55:28 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:55:30 Initializing from normalized Laplacian + noise (using RSpectra)
22:55:30 Commencing optimization for 500 epochs, with 48472 positive edges
22:55:30 Using rng type: pcg
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:55:32 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.74076962471008
UMAP plot: DONE
* checking uniformity of cluster '0' of 2 clusters
Asked to drop 0 genes and 587 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [613] cells
Dataset cleaning elapsed time: 0.962116241455078
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 1.95056486129761
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0334270578203965 | max: 8.68674670630126 | % negative: 4.16666666666667
Model parameter estimation elapsed time: 2.82032155990601
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 8.60947275161743
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00536465644836426
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0415356159210205
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.82303524017334
Total calculations elapsed time: 9.47940826416016
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 10.3157186508179
Dataset analysis elapsed time: 14.098156452179
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0000' with 613 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0321862697601318
Calculate `GDI`: DONE
Total calculations elapsed time: 2.73719167709351
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0367176532745361
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0000, with size 613, is uniform
Cluster 01_0000's shift to uniformity: -0.0159698218977267
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0333333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38103017810227, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0233333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42514299918545, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.45038824726242, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 2, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.50155519585851, isUniform = TRUE, clusterSize = 613
cluster 01_0000 is uniform
* checking uniformity of cluster '1' of 2 clusters
Asked to drop 0 genes and 613 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [587] cells
Dataset cleaning elapsed time: 0.895963668823242
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 1.98155379295349
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0383377991708709 | max: 19.013469852533 | % negative: 7
Model parameter estimation elapsed time: 2.83936071395874
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 8.57374596595764
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00534725189208984
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0373852252960205
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.937093496322632
Total calculations elapsed time: 9.55357193946838
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 10.4268243312836
Dataset analysis elapsed time: 14.1621487140656
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0001' with 587 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0322408676147461
Calculate `GDI`: DONE
Total calculations elapsed time: 2.74176716804504
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0347070693969727
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 587, is uniform
Cluster 01_0001's shift to uniformity: -0.00930197949809752
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0433333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.3876980205019, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42646635133468, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00833333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.46799318315157, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 5, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.52850104542574, isUniform = TRUE, clusterSize = 587
cluster 01_0001 is uniform
Found 2 uniform and 0 non-uniform clusters
Stopping: too few cells left to cluster
Unclustered cell left: 0
The final raw clusterization contains [ 2 ] different clusters: 01_0000, 01_0001
Differential Expression Analysis - START
* DEA on cluster '1' with 613 cells
* DEA on cluster '2' with 587 cells
Total calculations elapsed time: 0.0695095062255859
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Total calculations elapsed time: 58.0627295970917
Creating cells' uniform clustering: DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Asked to drop 0 genes and 613 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [587] cells
Dataset cleaning elapsed time: 0.866128921508789
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 1.94052362442017
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0383377991708709 | max: 19.013469852533 | % negative: 7
Model parameter estimation elapsed time: 2.88758301734924
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 9.65520429611206
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00946283340454102
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0422995090484619
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.13619542121887
Total calculations elapsed time: 10.8431620597839
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 11.8704097270966
Dataset analysis elapsed time: 15.6241216659546
COTAN dataset analysis: DONE
Checking uniformity for the cluster 'Cluster_2' with 587 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0370109081268311
Calculate `GDI`: DONE
Total calculations elapsed time: 2.84109449386597
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0348091125488281
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster Cluster_2, with size 587, is uniform
Cluster Cluster_2's shift to uniformity: -0.00930197949809752
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0433333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.3876980205019, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42646635133468, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00833333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.46799318315157, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 5, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.52850104542574, isUniform = TRUE, clusterSize = 587
Differential Expression Analysis - START
* DEA on cluster '-1' with 50 cells
* DEA on cluster '1' with 611 cells
* DEA on cluster '2' with 539 cells
Total calculations elapsed time: 0.0760183334350586
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 2, 2 -> 1, -1 -> -1
Applied reordering to clusterization is:
1 -> 1, 2 -> 2, -1 -> -1
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Asked to drop no genes or cells
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0395462512969971
Calculate `GDI`: DONE
Total calculations elapsed time: 2.88371539115906
Calculate GDI dataframe: DONE
Included 186 genes with GDI below 1.3
Selected 600 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 5.67361044883728
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 55489
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
Total calculations elapsed time: 6.52568364143372
Creating new clusterization: DONE
Using passed in clusterization
Creating PDF UMAP in file: /tmp/Rtmp1jq8Pz/test/reclustering/pdf_umap_1.pdf
UMAP plot: START
Calculating UMAP: START
22:56:43 UMAP embedding parameters a = 0.9922 b = 1.112
22:56:43 Read 1200 rows and found 40 numeric columns
22:56:43 Using Annoy for neighbor search, n_neighbors = 30
22:56:43 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:56:43 Writing NN index file to temp file /tmp/Rtmp1jq8Pz/file341eb9287a45f7
22:56:43 Searching Annoy index using 1 thread, search_k = 3000
22:56:44 Annoy recall = 100%
22:56:45 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:56:46 Initializing from normalized Laplacian + noise (using RSpectra)
22:56:46 Commencing optimization for 500 epochs, with 42644 positive edges
22:56:46 Using rng type: pcg
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:56:49 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.75074625015259
UMAP plot: DONE
UMAP plot: START
Calculating UMAP: START
22:56:49 UMAP embedding parameters a = 0.9922 b = 1.112
22:56:49 Read 1200 rows and found 40 numeric columns
22:56:49 Using Annoy for neighbor search, n_neighbors = 30
22:56:49 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:56:49 Writing NN index file to temp file /tmp/Rtmp1jq8Pz/file341eb94259303a
22:56:49 Searching Annoy index using 1 thread, search_k = 3000
22:56:50 Annoy recall = 100%
22:56:50 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:56:52 Initializing from normalized Laplacian + noise (using RSpectra)
22:56:52 Commencing optimization for 500 epochs, with 42644 positive edges
22:56:52 Using rng type: pcg
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:56:55 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.79486465454102
UMAP plot: DONE
* checking uniformity of cluster '1' of 2 clusters
Asked to drop 0 genes and 600 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [600] cells
Dataset cleaning elapsed time: 0.956506013870239
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 1.8387176990509
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0387079873074399 | max: 19.3963889884382 | % negative: 6.5
Model parameter estimation elapsed time: 2.69634222984314
COTAN genes' COEX estimation: START
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 8.61761474609375
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0053253173828125
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0368294715881348
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.8460853099823
Total calculations elapsed time: 9.505854845047
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 10.3556900024414
Dataset analysis elapsed time: 14.0085382461548
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0001' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0321760177612305
Calculate `GDI`: DONE
Total calculations elapsed time: 2.59042596817017
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.034308910369873
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 600, is uniform
Cluster 01_0001's shift to uniformity: -0.0123041937719002
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0383333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.3846958062281, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.035, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42417208332107, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00666666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.45335006989432, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 4, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.51519118633036, isUniform = TRUE, clusterSize = 600
cluster 01_0001 is uniform
* checking uniformity of cluster '2' of 2 clusters
Asked to drop 0 genes and 600 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [600] cells
Dataset cleaning elapsed time: 0.88222599029541
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 1.88153052330017
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0329292435898063 | max: 10.0824885336881 | % negative: 3.66666666666667
Model parameter estimation elapsed time: 2.74263620376587
COTAN genes' COEX estimation: START
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 8.29088377952576
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0052647590637207
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0413799285888672
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.873497247695923
Total calculations elapsed time: 9.21102571487427
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 10.1117928028107
Dataset analysis elapsed time: 13.7366549968719
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0002' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.032127857208252
Calculate `GDI`: DONE
Total calculations elapsed time: 2.56690812110901
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0348479747772217
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 600, is uniform
Cluster 01_0002's shift to uniformity: -0.0203364702469158
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0366666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37666352975308, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42307834225193, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.43781655605474, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 2, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.50180130506577, isUniform = TRUE, clusterSize = 600
cluster 01_0002 is uniform
Found 2 uniform and 0 non-uniform clusters
Stopping: too few cells left to cluster
Unclustered cell left: 0
The final raw clusterization contains [ 2 ] different clusters: 01_0001, 01_0002
Differential Expression Analysis - START
* DEA on cluster '1' with 600 cells
* DEA on cluster '2' with 600 cells
Total calculations elapsed time: 0.0694241523742676
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Total calculations elapsed time: 59.3724937438965
Creating cells' uniform clustering: DONE
findClustersMarkers - START
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
Total calculations elapsed time: 1.83899283409119
Log Fold Change Analysis - DONE
Total calculations elapsed time: 1.84711003303528
findClustersMarkers - DONE
findClustersMarkers - START
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
Total calculations elapsed time: 2.13515543937683
Log Fold Change Analysis - DONE
Total calculations elapsed time: 2.14299988746643
findClustersMarkers - DONE
findClustersMarkers - START
Differential Expression Analysis - START
* DEA on cluster '1' with 613 cells
* DEA on cluster '2' with 587 cells
Total calculations elapsed time: 0.078831672668457
Differential Expression Analysis - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
Total calculations elapsed time: 2.15254807472229
Log Fold Change Analysis - DONE
Total calculations elapsed time: 2.23800563812256
findClustersMarkers - DONE
[1] "Tested cluster: 1"
Asked to drop 0 genes and 587 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [613] cells
Dataset cleaning elapsed time: 1.03422164916992
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.15901017189026
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0334270578203965 | max: 8.68674670630126 | % negative: 4.16666666666667
Model parameter estimation elapsed time: 3.2258574962616
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 8.76166272163391
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00515484809875488
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0403850078582764
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.78838038444519
Total calculations elapsed time: 9.59558296203613
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 10.3931615352631
Dataset analysis elapsed time: 14.6532406806946
COTAN dataset analysis: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0316131114959717
Calculate `GDI`: DONE
Total calculations elapsed time: 2.40834808349609
Calculate GDI dataframe: DONE
[1] "Tested cluster: 2"
Asked to drop 0 genes and 613 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [587] cells
Dataset cleaning elapsed time: 0.811495304107666
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 1.72877931594849
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0383377991708709 | max: 19.013469852533 | % negative: 7
Model parameter estimation elapsed time: 2.55507016181946
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 8.50862216949463
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00524353981018066
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0371341705322266
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.895994186401367
Total calculations elapsed time: 9.4469940662384
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 10.3790366649628
Dataset analysis elapsed time: 13.7456021308899
COTAN dataset analysis: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0322532653808594
Calculate `GDI`: DONE
Total calculations elapsed time: 2.72802042961121
Calculate GDI dataframe: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 1.98646950721741
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 0.83634877204895
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 1.94046211242676
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 2.88119029998779
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.933470249176025
Dataset analysis elapsed time: 4.65100932121277
COTAN dataset analysis: DONE
Normalizing layer: counts
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix
|
| | 0%
|
|======================================================================| 100%
PC_ 1
Positive: g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528
g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583
g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541
Negative: g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140
g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135
g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128
PC_ 2
Positive: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539
g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538
g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570
Negative: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087
g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207
g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158
PC_ 3
Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360
g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470
g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317
Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303
g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262
g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241
PC_ 4
Positive: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079
g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228
g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150
Negative: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131
g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366
g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306
PC_ 5
Positive: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237
g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505
g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393
Negative: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578
g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381
g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 55884
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5927
Number of communities: 4
Elapsed time: 0 seconds
Clusterizations found: RNA_snn_res.0.8, seurat_clusters
Conditions found: orig.ident
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 0.906024932861328
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 1.9818971157074
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 2.84392857551575
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.906639575958252
Dataset analysis elapsed time: 4.65659308433533
COTAN dataset analysis: DONE
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 0.856094598770142
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.04169702529907
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 3.03729772567749
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 9.24312305450439
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00585675239562988
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0511677265167236
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.06625366210938
Total calculations elapsed time: 10.3664011955261
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 11.3854658603668
Dataset analysis elapsed time: 15.2788581848145
COTAN dataset analysis: DONE
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
Total calculations elapsed time: 0.00513505935668945
calculating PValues: DONE
Number of selected secondary markers: 6
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00856423377990723
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 6
Number of rows (U set): 60
Total calculations elapsed time: 1.02037811279297
Calculating gene co-expression space - DONE
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
Total calculations elapsed time: 0.00711202621459961
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00969696044921875
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
Total calculations elapsed time: 0.968994140625
Calculating gene co-expression space - DONE
Establishing gene clusters - START
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
Total calculations elapsed time: 0.00875353813171387
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00960755348205566
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
Total calculations elapsed time: 1.04091930389404
Calculating gene co-expression space - DONE
Total calculations elapsed time: 1.10505986213684
Establishing gene clusters - DONE
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 0.949464797973633
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.01862978935242
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 2.91951942443848
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.95222544670105
Dataset analysis elapsed time: 4.82120966911316
COTAN dataset analysis: DONE
Differential Expression Analysis - START
* DEA on cluster '1' with 608 cells
* DEA on cluster '2' with 592 cells
Total calculations elapsed time: 0.0784904956817627
Differential Expression Analysis - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
Total calculations elapsed time: 2.44911909103394
Log Fold Change Analysis - DONE
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.09087489420394
Handling cluster '2' with mean UDE 0.906669027574328
clustersDeltaExpression - DONE
In group G1 there are 3 detected over 3 genes
In group G2 there are 2 detected over 3 genes
In group G3 there are 5 detected over 5 genes
Merging cells' uniform clustering: START
The merge algorithm will use 2 passes
Start merging nearest clusters - the main threshold is: 1.297
Start merging nearest clusters: iteration 1
Differential Expression Analysis - START
* DEA on cluster '1' with 608 cells
* DEA on cluster '2' with 592 cells
Total calculations elapsed time: 0.0715327262878418
Differential Expression Analysis - DONE
Updating check results for the 0 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("1", "2")
*1_2-merge
Asked to drop no genes or cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Dataset cleaning elapsed time: 0.882646799087524
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 1.92658925056458
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.219880139527933 | max: 6.08024473714308 | % negative: 0
Model parameter estimation elapsed time: 2.79243135452271
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 9.27410078048706
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00633597373962402
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0530776977539062
Estimating genes' COEX
Calculate genes' COEX elapsed time: 1.05993175506592
Total calculations elapsed time: 10.3934462070465
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 11.3969674110413
Dataset analysis elapsed time: 15.0720455646515
COTAN dataset analysis: DONE
Checking uniformity for the cluster '1_2-merge' with 1200 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0320277214050293
Calculate `GDI`: DONE
Total calculations elapsed time: 2.79617142677307
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0347940921783447
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge, with size 1200, is not uniform
Cluster 1_2-merge's shift to uniformity: 0.273171158219278
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.696666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.57017115821928, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.665, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.61241976619327, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.411666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.64049230721131, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 247, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.66511539543561, isUniform = FALSE, clusterSize = 1200
Clusters 1 and 2 cannot be merged
Finished the first batch - no merges were executed
Loop calculations elapsed time: 22.5668668746948
Start merging nearest clusters: iteration 2
Differential Expression Analysis - START
* DEA on cluster '1' with 608 cells
* DEA on cluster '2' with 592 cells
Total calculations elapsed time: 0.0906262397766113
Differential Expression Analysis - DONE
Updating check results for the 1 already tested pairs to align to new checker
0 new clusters pairs to be tested for merging:
No clusters will be merged
None of the remaining tested cluster pairs could be merged
Executed all merges for threshold 1.297 out of 1 checks
Start merging nearest clusters - the main threshold is: 1.397
Start merging nearest clusters: iteration 3
Differential Expression Analysis - START
* DEA on cluster '1' with 608 cells
* DEA on cluster '2' with 592 cells
Total calculations elapsed time: 0.0761537551879883
Differential Expression Analysis - DONE
Updating check results for the 1 already tested pairs to align to new checker
0 new clusters pairs to be tested for merging:
No clusters will be merged
None of the remaining tested cluster pairs could be merged
Executed all merges for threshold 1.397 out of 1 checks
The final merged clusterization contains [2] different clusters: 1, 2
Differential Expression Analysis - START
* DEA on cluster '1' with 608 cells
* DEA on cluster '2' with 592 cells
Total calculations elapsed time: 0.0736846923828125
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Total calculations elapsed time: 24.7870488166809
Merging cells' uniform clustering: DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
Total calculations elapsed time: 1.82740759849548
Log Fold Change Analysis - DONE
[1] "Tested cluster: 1"
Asked to drop 0 genes and 592 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [608] cells
Dataset cleaning elapsed time: 0.999625682830811
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 2.12973642349243
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0337582853418583 | max: 10.9273420652532 | % negative: 4.33333333333333
Model parameter estimation elapsed time: 2.97616672515869
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 8.78444170951843
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00556826591491699
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0409045219421387
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.933499097824097
Total calculations elapsed time: 9.76441359519958
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 10.7009530067444
Dataset analysis elapsed time: 14.6767454147339
COTAN dataset analysis: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0343630313873291
Calculate `GDI`: DONE
Total calculations elapsed time: 2.86834073066711
Calculate GDI dataframe: DONE
[1] "Tested cluster: 2"
Asked to drop 0 genes and 608 cells
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [592] cells
Dataset cleaning elapsed time: 0.879945278167725
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 4 iterations
Total calculations elapsed time: 1.90501356124878
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0390500444479481 | max: 19.2061656068405 | % negative: 7.33333333333333
Model parameter estimation elapsed time: 2.77538561820984
COTAN genes' COEX estimation: START
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 9.074538230896
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00594735145568848
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0391058921813965
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.902203559875488
Total calculations elapsed time: 10.0217950344086
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 10.9359073638916
Dataset analysis elapsed time: 14.5912382602692
COTAN dataset analysis: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.0346970558166504
Calculate `GDI`: DONE
Total calculations elapsed time: 2.91223669052124
Calculate GDI dataframe: DONE
Dispersion bisection: straddling used 2 iterations
Dispersion bisection: used 8 iterations
Dispersion bisection: straddling used 1 iterations
Dispersion bisection: used 9 iterations
Dispersion Newton-Raphson: used up to 4 iterations
Dispersion Newton-Raphson: used up to 4 iterations
parallel dispersion bisection: straddling used up to 2 iterations
Parallel dispersion bisection: used up to 9 iterations
Parallel dispersion Newton-Raphson: used up to 4 iterations
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 572 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 572 ]
>
> proc.time()
user system elapsed
6286.633 20.497 723.871
COTAN.Rcheck/COTAN-Ex.timings
| name | user | system | elapsed | |
| COTAN_Legacy | 0.003 | 0.000 | 0.003 | |
| COTAN_ObjectCreation | 360.246 | 0.703 | 22.139 | |
| CalculatingCOEX | 1294.958 | 2.374 | 91.824 | |
| ClustersList | 0.008 | 0.000 | 0.008 | |
| Conversions | 5.060 | 0.076 | 5.136 | |
| GenesStatistics | 304.618 | 0.980 | 16.014 | |
| HandleMetaData | 0.071 | 0.002 | 0.073 | |
| HandlingClusterizations | 339.088 | 0.847 | 47.387 | |
| HandlingConditions | 0.090 | 0.001 | 0.091 | |
| HeatmapPlots | 884.324 | 0.934 | 47.502 | |
| Installing_torch | 0 | 0 | 0 | |
| LoggingFunctions | 0.001 | 0.000 | 0.002 | |
| ParametersEstimations | 25.376 | 0.302 | 23.873 | |
| RawDataCleaning | 4.441 | 0.006 | 4.380 | |
| RawDataGetters | 0.071 | 0.000 | 0.070 | |
| UniformClusters | 2189.895 | 6.134 | 161.828 | |
| getColorsVector | 0.001 | 0.000 | 0.001 | |