Back to Multiple platform build/check report for BioC 3.22: simplified long |
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This page was generated on 2025-10-14 12:03 -0400 (Tue, 14 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" | 4864 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4652 |
kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4597 |
taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4610 |
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 1559/2346 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
peakCombiner 0.99.602 (landing page) Markus Muckenhuber
| 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 peakCombiner package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/peakCombiner.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: peakCombiner |
Version: 0.99.602 |
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:peakCombiner.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings peakCombiner_0.99.602.tar.gz |
StartedAt: 2025-10-14 03:05:16 -0400 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 03:07:11 -0400 (Tue, 14 Oct 2025) |
EllapsedTime: 115.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: peakCombiner.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:peakCombiner.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings peakCombiner_0.99.602.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/peakCombiner.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 ‘peakCombiner/DESCRIPTION’ ... OK * this is package ‘peakCombiner’ version ‘0.99.602’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘peakCombiner’ 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 dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘GenomeInfoDb’ All declared Imports should be used. * 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 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... 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: 1 NOTE See ‘/home/biocbuild/bbs-3.22-bioc/meat/peakCombiner.Rcheck/00check.log’ for details.
peakCombiner.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL peakCombiner ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’ * installing *source* package ‘peakCombiner’ ... ** this is package ‘peakCombiner’ version ‘0.99.602’ ** 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 (peakCombiner)
peakCombiner.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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(peakCombiner) > > test_check("peakCombiner") ℹ Argument `outputFormat` is set to "tibble". ℹ Argument `startsAreBased` is 1. ℹ Argument `starts.in.df.are.0based` is FALSE. ℹ Provide input `data` is a pre-loaded <data.frame> with the required column names. → Start preparing data. ℹ Required columns will be added if missing. ! Column 'score' does not exist in `data_prepared`. → Column 'score' is added and filled with "0". ! Column 'strand' does not exist in `data_prepared`. → Column 'strand' is added and filled with ".". ! Column 'summit' does not exist in `data_prepared`. → As no input column 'summit' is found, the output column 'center' has to be filled with arithmetic center of peak. → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. → Checking whether duplicated regions exist and need to be collapsed. → Checked whether duplicated regions exist and need to be collapsed. ✔ Duplicated regions identified and collapsed to unique chrom, start, and end for each sample by strongest score value. ✔ Preparation of data finished successfully. ℹ Output format is set to "tibble". # A tibble: 51 × 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 441 458 control_rep1|9 0 . 450 control_rep1 2 chr1 641 658 control_rep1|1 0 . 650 control_rep1 3 chr1 3941 3958 control_rep1|2 0 . 3950 control_rep1 4 chr1 4991 5008 control_rep1|4 0 . 5000 control_rep1 5 chr1 5841 5858 control_rep1|5 0 . 5850 control_rep1 6 chr1 7041 7058 control_rep1|6 0 . 7050 control_rep1 7 chr10 641 658 control_rep1|7 0 . 650 control_rep1 8 chr2 641 658 control_rep1|8 0 . 650 control_rep1 9 chr4 2 641 658 control_rep1|10 0 . 650 control_rep1 10 chr4-2 741 758 control_rep1|11 0 . 750 control_rep1 # ℹ 41 more rows # A tibble: 42 × 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 chr1 559 738 control_rep1|1 0 . 650 control_rep1 2 chr1 3859 4038 control_rep1|2 0 . 3950 control_rep1 3 chr1 4909 5088 control_rep1|4 0 . 5000 control_rep1 4 chr1 5759 5938 control_rep1|5 0 . 5850 control_rep1 5 chr1 6959 7138 control_rep1|6 0 . 7050 control_rep1 6 chr10 559 738 control_rep1|7 0 . 650 control_rep1 7 chr2 559 738 control_rep1|8 0 . 650 control_rep1 8 chr1 109 288 control_rep2|1 0 . 200 control_rep2 9 chr1 509 688 control_rep2|2 0 . 600 control_rep2 10 chr1 3759 3938 control_rep2|3 0 . 3850 control_rep2 # ℹ 32 more rows # A tibble: 8 × 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 chr1 498 701 combined|1 0 . 600 combined 2 chr1 2798 3001 combined|2 0 . 2900 combined 3 chr1 3848 4051 combined|3 0 . 3950 combined 4 chr1 4798 5001 combined|4 0 . 4900 combined 5 chr1 5948 6151 combined|5 0 . 6050 combined 6 chr1 6948 7151 combined|6 0 . 7050 combined 7 chr2 448 651 combined|7 0 . 550 combined 8 chr10 448 651 combined|8 0 . 550 combined # A tibble: 42 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 chr1 300 999 control_rep1|1 0 . 650 control_rep1 2 chr1 3600 4299 control_rep1|2 0 . 3950 control_rep1 3 chr1 4650 5349 control_rep1|4 0 . 5000 control_rep1 4 chr1 5500 6199 control_rep1|5 0 . 5850 control_rep1 5 chr1 6700 7399 control_rep1|6 0 . 7050 control_rep1 6 chr10 300 999 control_rep1|7 0 . 650 control_rep1 7 chr2 300 999 control_rep1|8 0 . 650 control_rep1 8 chr1 1 549 control_rep2|1 0 . 200 control_rep2 9 chr1 250 949 control_rep2|2 0 . 600 control_rep2 10 chr1 3500 4199 control_rep2|3 0 . 3850 control_rep2 # i 32 more rows # A tibble: 42 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 chr1 300 999 control_rep1|1 0 . 650 control_rep1 2 chr1 3600 4299 control_rep1|2 0 . 3950 control_rep1 3 chr1 4650 5349 control_rep1|4 0 . 5000 control_rep1 4 chr1 5500 6199 control_rep1|5 0 . 5850 control_rep1 5 chr1 6700 7399 control_rep1|6 0 . 7050 control_rep1 6 chr10 300 999 control_rep1|7 0 . 650 control_rep1 7 chr2 300 999 control_rep1|8 0 . 650 control_rep1 8 chr1 1 549 control_rep2|1 0 . 200 control_rep2 9 chr1 250 949 control_rep2|2 0 . 600 control_rep2 10 chr1 3500 4199 control_rep2|3 0 . 3850 control_rep2 # i 32 more rows # A tibble: 51 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 100 799 control_rep1|9 0 . 450 control_rep1 2 chr1 300 999 control_rep1|1 0 . 650 control_rep1 3 chr1 3600 4299 control_rep1|2 0 . 3950 control_rep1 4 chr1 4650 5349 control_rep1|4 0 . 5000 control_rep1 5 chr1 5500 6199 control_rep1|5 0 . 5850 control_rep1 6 chr1 6700 7399 control_rep1|6 0 . 7050 control_rep1 7 chr10 300 999 control_rep1|7 0 . 650 control_rep1 8 chr2 300 999 control_rep1|8 0 . 650 control_rep1 9 chr4 2 300 999 control_rep1|10 0 . 650 control_rep1 10 chr4-2 400 1099 control_rep1|11 0 . 750 control_rep1 # i 41 more rows i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. v `expandBy` was calculated from the input data and set to "350". i Genomic regions will be expanded by 350bp in both direction. i Argument `outputFormat` is set to "tibble". i Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). i Argument `genome` set to NA. i Only start will be trimmed. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `trim_start` is FALSE. > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. > Starting with expanding genomic regions from the column center. > Genomic regions will be centered and expanded. i Used genome for trimming is NA. > Expanding genomic regions from the column center by 350 before and 350 after the center. # A tibble: 51 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 100 799 control_rep1|9 0 . 450 control_rep1 2 chr1 300 999 control_rep1|1 0 . 650 control_rep1 3 chr1 3600 4299 control_rep1|2 0 . 3950 control_rep1 4 chr1 4650 5349 control_rep1|4 0 . 5000 control_rep1 5 chr1 5500 6199 control_rep1|5 0 . 5850 control_rep1 6 chr1 6700 7399 control_rep1|6 0 . 7050 control_rep1 7 chr10 300 999 control_rep1|7 0 . 650 control_rep1 8 chr2 300 999 control_rep1|8 0 . 650 control_rep1 9 chr4 2 300 999 control_rep1|10 0 . 650 control_rep1 10 chr4-2 400 1099 control_rep1|11 0 . 750 control_rep1 # i 41 more rows v Genomic regions were successfully centered and expanded. v Genomic regions were successfully centered and expanded. i Output format is set to "tibble". i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. v `expandBy` was calculated from the input data and set to "102". i Genomic regions will be expanded by 102bp in both direction. i Argument `outputFormat` is set to "tibble". i Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). i Argument `genome` set to NA. i Only start will be trimmed. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `trim_start` is FALSE. > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. > Starting with expanding genomic regions from the column center. > Genomic regions will be centered and expanded. i Used genome for trimming is NA. > Expanding genomic regions from the column center by 102 before and 102 after the center. # A tibble: 8 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 chr1 498 701 combined|1 0 . 600 combined 2 chr1 2798 3001 combined|2 0 . 2900 combined 3 chr1 3848 4051 combined|3 0 . 3950 combined 4 chr1 4798 5001 combined|4 0 . 4900 combined 5 chr1 5948 6151 combined|5 0 . 6050 combined 6 chr1 6948 7151 combined|6 0 . 7050 combined 7 chr2 448 651 combined|7 0 . 550 combined 8 chr10 448 651 combined|8 0 . 550 combined v Genomic regions were successfully centered and expanded. v Genomic regions were successfully centered and expanded. i Output format is set to "tibble". i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. v `expandBy` was calculated from the input data and set to "350". i Genomic regions will be expanded by 350bp in both direction. i Argument `outputFormat` is set to "tibble". i Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). i Argument `genome` set to NA. i Only start will be trimmed. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `trim_start` is FALSE. > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. > Starting with expanding genomic regions from the column center. > Genomic regions will be centered and expanded. i Used genome for trimming is NA. > Expanding genomic regions from the column center by 350 before and 350 after the center. # A tibble: 51 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 100 799 control_rep1|9 0 . 450 control_rep1 2 chr1 300 999 control_rep1|1 0 . 650 control_rep1 3 chr1 3600 4299 control_rep1|2 0 . 3950 control_rep1 4 chr1 4650 5349 control_rep1|4 0 . 5000 control_rep1 5 chr1 5500 6199 control_rep1|5 0 . 5850 control_rep1 6 chr1 6700 7399 control_rep1|6 0 . 7050 control_rep1 7 chr10 300 999 control_rep1|7 0 . 650 control_rep1 8 chr2 300 999 control_rep1|8 0 . 650 control_rep1 9 chr4 2 300 999 control_rep1|10 0 . 650 control_rep1 10 chr4-2 400 1099 control_rep1|11 0 . 750 control_rep1 # i 41 more rows v Genomic regions were successfully centered and expanded. v Genomic regions were successfully centered and expanded. i Output format is set to "tibble". i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. v `expandBy` was calculated from the input data and set to "350". i Genomic regions will be expanded by 350bp in both direction. i Argument `outputFormat` is set to "tibble". i Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). i Argument `genome` set to NA. i Only start will be trimmed. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `trim_start` is FALSE. i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. v `expandBy` was calculated from the input data and set to "350". i Genomic regions will be expanded by 350bp in both direction. i Argument `outputFormat` is set to "tibble". i Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). i Argument `genome` set to NA. i Only start will be trimmed. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `trim_start` is FALSE. i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. v `expandBy` was calculated from the input data and set to "350". i Genomic regions will be expanded by 350bp in both direction. i Argument `outputFormat` is set to "tibble". i Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). i Argument `genome` set to NA. i Only start will be trimmed. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `trim_start` is FALSE. i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. v `expandBy` was calculated from the input data and set to "350". i Genomic regions will be expanded by 350bp in both direction. i Argument `outputFormat` is set to "tibble". i Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). i Argument `genome` set to NA. i Only start will be trimmed. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `trim_start` is FALSE. i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. v `expandBy` was calculated from the input data and set to "350". i Genomic regions will be expanded by 350bp in both direction. i Argument `outputFormat` is set to "tibble". i Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). i Argument `genome` set to NA. i Only start will be trimmed. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `trim_start` is FALSE. > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. > Starting with expanding genomic regions from the column center. > Genomic regions will be centered and expanded. i Used genome for trimming is NA. > Expanding genomic regions from the column center by 350 before and 350 after the center. # A tibble: 51 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 100 799 control_rep1|9 0 . 450 control_rep1 2 chr1 300 999 control_rep1|1 0 . 650 control_rep1 3 chr1 3600 4299 control_rep1|2 0 . 3950 control_rep1 4 chr1 4650 5349 control_rep1|4 0 . 5000 control_rep1 5 chr1 5500 6199 control_rep1|5 0 . 5850 control_rep1 6 chr1 6700 7399 control_rep1|6 0 . 7050 control_rep1 7 chr10 300 999 control_rep1|7 0 . 650 control_rep1 8 chr2 300 999 control_rep1|8 0 . 650 control_rep1 9 chr4 2 300 999 control_rep1|10 0 . 650 control_rep1 10 chr4-2 400 1099 control_rep1|11 0 . 750 control_rep1 # i 41 more rows v Genomic regions were successfully centered and expanded. v Genomic regions were successfully centered and expanded. i Output format is set to "tibble". i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. v `expandBy` was calculated from the input data and set to "350". i Genomic regions will be expanded by 350bp in both direction. i Argument `outputFormat` is set to "tibble". i Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). i Argument `genome` set to NA. i Only start will be trimmed. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `trim_start` is FALSE. > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. > Starting with expanding genomic regions from the column center. > Genomic regions will be centered and expanded. i Used genome for trimming is NA. > Expanding genomic regions from the column center by 350 before and 350 after the center. # A tibble: 51 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 100 799 control_rep1|9 0 . 450 control_rep1 2 chr1 300 999 control_rep1|1 0 . 650 control_rep1 3 chr1 3600 4299 control_rep1|2 0 . 3950 control_rep1 4 chr1 4650 5349 control_rep1|4 0 . 5000 control_rep1 5 chr1 5500 6199 control_rep1|5 0 . 5850 control_rep1 6 chr1 6700 7399 control_rep1|6 0 . 7050 control_rep1 7 chr10 300 999 control_rep1|7 0 . 650 control_rep1 8 chr2 300 999 control_rep1|8 0 . 650 control_rep1 9 chr4 2 300 999 control_rep1|10 0 . 650 control_rep1 10 chr4-2 400 1099 control_rep1|11 0 . 750 control_rep1 # i 41 more rows v Genomic regions were successfully centered and expanded. v Genomic regions were successfully centered and expanded. i Output format is set to "tibble". i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. v `expandBy` was calculated from the input data and set to "350". i Genomic regions will be expanded by 350bp in both direction. i Argument `outputFormat` is set to "tibble". i Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). i Argument `genome` set to NA. i Only start will be trimmed. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `trim_start` is FALSE. > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. > Starting with expanding genomic regions from the column center. > Genomic regions will be centered and expanded. i Used genome for trimming is NA. > Expanding genomic regions from the column center by 350 before and 350 after the center. # A tibble: 51 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 100 799 control_rep1|9 0 . 450 control_rep1 2 chr1 300 999 control_rep1|1 0 . 650 control_rep1 3 chr1 3600 4299 control_rep1|2 0 . 3950 control_rep1 4 chr1 4650 5349 control_rep1|4 0 . 5000 control_rep1 5 chr1 5500 6199 control_rep1|5 0 . 5850 control_rep1 6 chr1 6700 7399 control_rep1|6 0 . 7050 control_rep1 7 chr10 300 999 control_rep1|7 0 . 650 control_rep1 8 chr2 300 999 control_rep1|8 0 . 650 control_rep1 9 chr4 2 300 999 control_rep1|10 0 . 650 control_rep1 10 chr4-2 400 1099 control_rep1|11 0 . 750 control_rep1 # i 41 more rows v Genomic regions were successfully centered and expanded. v Genomic regions were successfully centered and expanded. i Output format is set to "tibble". i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. v `expandBy` was calculated from the input data and set to "90". i Genomic regions will be expanded by 90bp in both direction. i Argument `outputFormat` is set to "tibble". i Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). i Argument `genome` set to NA. i Only start will be trimmed. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `trim_start` is FALSE. > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. > Starting with expanding genomic regions from the column center. > Genomic regions will be centered and expanded. i Used genome for trimming is NA. > Expanding genomic regions from the column center by 90 before and 90 after the center. # A tibble: 42 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 chr1 560 739 control_rep1|1 0 . 650 control_rep1 2 chr1 3860 4039 control_rep1|2 0 . 3950 control_rep1 3 chr1 4910 5089 control_rep1|4 0 . 5000 control_rep1 4 chr1 5760 5939 control_rep1|5 0 . 5850 control_rep1 5 chr1 6960 7139 control_rep1|6 0 . 7050 control_rep1 6 chr10 560 739 control_rep1|7 0 . 650 control_rep1 7 chr2 560 739 control_rep1|8 0 . 650 control_rep1 8 chr1 110 289 control_rep2|1 0 . 200 control_rep2 9 chr1 510 689 control_rep2|2 0 . 600 control_rep2 10 chr1 3760 3939 control_rep2|3 0 . 3850 control_rep2 # i 32 more rows v Genomic regions were successfully centered and expanded. v Genomic regions were successfully centered and expanded. i Output format is set to "tibble". i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. v `expandBy` was calculated from the input data and set to "90". i Genomic regions will be expanded by 90bp in both direction. i Argument `outputFormat` is set to "tibble". i Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). i Argument `genome` set to NA. i Only start will be trimmed. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `trim_start` is FALSE. > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. > Starting with expanding genomic regions from the column center. > Genomic regions will be centered and expanded. i Used genome for trimming is NA. > Expanding genomic regions from the column center by 90 before and 90 after the center. # A tibble: 42 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 chr1 560 739 control_rep1|1 0 . 650 control_rep1 2 chr1 3860 4039 control_rep1|2 0 . 3950 control_rep1 3 chr1 4910 5089 control_rep1|4 0 . 5000 control_rep1 4 chr1 5760 5939 control_rep1|5 0 . 5850 control_rep1 5 chr1 6960 7139 control_rep1|6 0 . 7050 control_rep1 6 chr10 560 739 control_rep1|7 0 . 650 control_rep1 7 chr2 560 739 control_rep1|8 0 . 650 control_rep1 8 chr1 110 289 control_rep2|1 0 . 200 control_rep2 9 chr1 510 689 control_rep2|2 0 . 600 control_rep2 10 chr1 3760 3939 control_rep2|3 0 . 3850 control_rep2 # i 32 more rows v Genomic regions were successfully centered and expanded. v Genomic regions were successfully centered and expanded. i Output format is set to "tibble". i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. v `expandBy` was calculated from the input data and set to "90". i Genomic regions will be expanded by 90bp in both direction. i Argument `outputFormat` is set to "tibble". i Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). i Argument `genome` set to NA. i Only start will be trimmed. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `trim_start` is FALSE. > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. > Starting with expanding genomic regions from the column center. > Genomic regions will be centered and expanded. i Used genome for trimming is NA. > Expanding genomic regions from the column center by 90 before and 90 after the center. # A tibble: 42 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 chr1 560 739 control_rep1|1 0 . 650 control_rep1 2 chr1 3860 4039 control_rep1|2 0 . 3950 control_rep1 3 chr1 4910 5089 control_rep1|4 0 . 5000 control_rep1 4 chr1 5760 5939 control_rep1|5 0 . 5850 control_rep1 5 chr1 6960 7139 control_rep1|6 0 . 7050 control_rep1 6 chr10 560 739 control_rep1|7 0 . 650 control_rep1 7 chr2 560 739 control_rep1|8 0 . 650 control_rep1 8 chr1 110 289 control_rep2|1 0 . 200 control_rep2 9 chr1 510 689 control_rep2|2 0 . 600 control_rep2 10 chr1 3760 3939 control_rep2|3 0 . 3850 control_rep2 # i 32 more rows v Genomic regions were successfully centered and expanded. v Genomic regions were successfully centered and expanded. i Output format is set to "tibble". i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. v `expandBy` was calculated from the input data and set to "90". i Genomic regions will be expanded by 90bp in both direction. i Argument `outputFormat` is set to "tibble". i Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). i Argument `genome` set to NA. i Only start will be trimmed. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `trim_start` is FALSE. > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. > Starting with expanding genomic regions from the column center. > Genomic regions will be centered and expanded. i Used genome for trimming is NA. > Expanding genomic regions from the column center by 90 before and 90 after the center. # A tibble: 42 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 chr1 560 739 control_rep1|1 0 . 650 control_rep1 2 chr1 3860 4039 control_rep1|2 0 . 3950 control_rep1 3 chr1 4910 5089 control_rep1|4 0 . 5000 control_rep1 4 chr1 5760 5939 control_rep1|5 0 . 5850 control_rep1 5 chr1 6960 7139 control_rep1|6 0 . 7050 control_rep1 6 chr10 560 739 control_rep1|7 0 . 650 control_rep1 7 chr2 560 739 control_rep1|8 0 . 650 control_rep1 8 chr1 110 289 control_rep2|1 0 . 200 control_rep2 9 chr1 510 689 control_rep2|2 0 . 600 control_rep2 10 chr1 3760 3939 control_rep2|3 0 . 3850 control_rep2 # i 32 more rows v Genomic regions were successfully centered and expanded. v Genomic regions were successfully centered and expanded. i Output format is set to "tibble". # A tibble: 8 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 chr1 496 699 combined|1 0 . 600 combined 2 chr1 2796 2999 combined|2 0 . 2900 combined 3 chr1 3846 4049 combined|3 0 . 3950 combined 4 chr1 4771 4974 combined|4 0 . 4900 combined 5 chr1 5946 6149 combined|5 0 . 6050 combined 6 chr1 6946 7149 combined|6 0 . 7050 combined 7 chr2 471 674 combined|7 0 . 550 combined 8 chr10 471 674 combined|8 0 . 550 combined # A tibble: 8 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 chr1 496 699 combined|1 0 . 600 combined 2 chr1 2796 2999 combined|2 0 . 2900 combined 3 chr1 3846 4049 combined|3 0 . 3950 combined 4 chr1 4771 4974 combined|4 0 . 4900 combined 5 chr1 5946 6149 combined|5 0 . 6050 combined 6 chr1 6946 7149 combined|6 0 . 7050 combined 7 chr2 471 674 combined|7 0 . 550 combined 8 chr10 471 674 combined|8 0 . 550 combined # A tibble: 42 x 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 chr1 300 999 control_rep1|1 0 . 650 control_rep1 2 chr1 3600 4299 control_rep1|2 0 . 3950 control_rep1 3 chr1 4650 5349 control_rep1|4 0 . 5000 control_rep1 4 chr1 5500 6199 control_rep1|5 0 . 5850 control_rep1 5 chr1 6700 7399 control_rep1|6 0 . 7050 control_rep1 6 chr10 300 999 control_rep1|7 0 . 650 control_rep1 7 chr2 300 999 control_rep1|8 0 . 650 control_rep1 8 chr1 1 549 control_rep2|1 0 . 200 control_rep2 9 chr1 250 949 control_rep2|2 0 . 600 control_rep2 10 chr1 3500 4199 control_rep2|3 0 . 3850 control_rep2 # i 32 more rows ℹ Argument `outputFormat` is set to "tibble". ℹ Argument `startsAreBased` is 1. ℹ Argument `starts.in.df.are.0based` is FALSE. ℹ Provide input `data` is a pre-loaded <data.frame> with the required column names. → Start preparing data. ℹ Required columns will be added if missing. ! Column 'name' from `data` will be overwritten. → Column 'name' is a computed column from peakCombiner and therefore pre-exisiting data in a column 'name' will not be retained. ! Column 'center' does exist in `data_prepared`. → The column 'center' is taken to define output column 'center'. → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. → Checking whether duplicated regions exist and need to be collapsed. → Checked whether duplicated regions exist and need to be collapsed. ✔ Duplicated regions identified and collapsed to unique chrom, start, and end for each sample by strongest score value. ✔ Preparation of data finished successfully. ℹ Output format is set to "tibble". ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. ✔ `expandBy` was calculated from the input data and set to "350". ℹ Genomic regions will be expanded by 350bp in both direction. ℹ Argument `outputFormat` is set to "tibble". ℹ Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). ℹ Argument `genome` set to NA. ℹ Only start will be trimmed. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `trim_start` is TRUE. → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. → Starting with expanding genomic regions from the column center. → Genomic regions will be centered and expanded. ℹ Used genome for trimming is NA. → Expanding genomic regions from the column center by 350 before and 350 after the center. # A tibble: 51 × 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 251 950 control_rep1|9 80 . 601 control_rep1 2 chr1 -49 650 control_rep1|1 96 . 301 control_rep1 3 chr1 -49 650 control_rep1|2 95 . 301 control_rep1 4 chr1 -149 550 control_rep1|3 46 . 201 control_rep1 5 chr1 -249 450 control_rep1|5 26 . 101 control_rep1 6 chr1 -49 650 control_rep1|6 25 . 301 control_rep1 7 chr10 -49 650 control_rep1|7 75 . 301 control_rep1 8 chr2 -49 650 control_rep1|8 50 . 301 control_rep1 9 chr4 2 -49 650 control_rep1|10 30 . 301 control_rep1 10 chr4-2 -149 550 control_rep1|11 20 . 201 control_rep1 # ℹ 41 more rows ✔ Genomic regions were successfully centered and expanded. ℹ Argument `trim_start` is set to "TRUE". ℹ Atgument `genome` is set to NA. → Trimming start coordinates of resulting genomic regions. ℹ Some newly-defined genomic regions have a start coordinate below "1". → Values of name for these sites: "control_rep1|1", "control_rep1|2", "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7", "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1", "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5", "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …, "treatment_rep3|5", and "treatment_rep3|8". ✔ These genomic regions were trimmed to get start coordinate "1". ✔ Genomic regions were successfully centered and expanded. ℹ Output format is set to "tibble". → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `outputFormat` is set to "tibble". ℹ The argument `includeByChromosomeName` is "NULL". ✔ No filtering for chromosome names in chrom is done. ℹ The argument `excludeByBlacklist` is "NULL". ✔ No filtering by blacklisted regions is done. ℹ The argument `includeAboveScoreCutoff` is "NULL". ✔ No filtering by score threshold is done. ℹ The argument `includeTopNScoring` is "NULL". ✔ No top enriched regions were selected. All input regions are retained. ✔ Filtered dataset will be returned. ℹ Output format is set to "tibble". ℹ Argument `outputFormat` is set to "tibble". ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. → Start with the disjoining and filtering genomic regions. ✔ Disjoin and filter by `foundInSamples` of genomic regions successfully finished. → Start with combining remaining genomic regions. ✔ Combining remaining genomic regions was successfully finished. → Start with identification of overlaps between the original summit and remaining genomic regions. ℹ Remaining regions without overlap will be removed. Joining with `by = join_by(ranking)` ✔ Retained genomic regions with input data summit overlap was successfully finished. → Information from input center will be added to output data frame. ℹ Argument `combinedCenter` was defined as "nearest". ℹ The mean of all input centers is calculated and the nearest input center is used → Center information in center and score are added to the output data frame. ✔ Output data frame columns center and score were successfully populated. → No value for column sample_name was provided. ℹ Column sample_name is filled with all input sample_names. ℹ Column name is created as unique identifier for each row containing sample_name and the row number. ✔ The columns sample_name and name were successfully populated. ℹ Argument `annotateWithInputNames` was set to "FALSE". ✔ Column input_names is not added to output data frame. ✔ All required columns in output data frame were successfully populated. ✔ Genomic regions were successfully combined. ℹ Output format is set to "tibble". i Argument `outputFormat` is set to "tibble". i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. > Start with the disjoining and filtering genomic regions. v Disjoin and filter by `foundInSamples` of genomic regions successfully finished. > Start with combining remaining genomic regions. v Combining remaining genomic regions was successfully finished. > Start with identification of overlaps between the original summit and remaining genomic regions. i Remaining regions without overlap will be removed. Joining with `by = join_by(ranking)` v Retained genomic regions with input data summit overlap was successfully finished. > Information from input center will be added to output data frame. i Argument `combinedCenter` was defined as "nearest". i The mean of all input centers is calculated and the nearest input center is used > Center information in center and score are added to the output data frame. v Output data frame columns center and score were successfully populated. > No value for column sample_name was provided. i Column sample_name is filled with all input sample_names. i Column name is created as unique identifier for each row containing sample_name and the row number. v The columns sample_name and name were successfully populated. i Argument `annotateWithInputNames` was set to "FALSE". v Column input_names is not added to output data frame. v All required columns in output data frame were successfully populated. v Genomic regions were successfully combined. i Output format is set to "tibble". > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. ✔ `expandBy` was calculated from the input data and set to "350". ℹ Genomic regions will be expanded by 350bp in both direction. ℹ Argument `outputFormat` is set to "tibble". ℹ Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). ℹ Argument `genome` set to NA. ℹ Only start will be trimmed. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `trim_start` is TRUE. → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. → Starting with expanding genomic regions from the column center. → Genomic regions will be centered and expanded. ℹ Used genome for trimming is NA. → Expanding genomic regions from the column center by 350 before and 350 after the center. # A tibble: 51 × 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 251 950 control_rep1|9 80 . 601 control_rep1 2 chr1 -49 650 control_rep1|1 96 . 301 control_rep1 3 chr1 -49 650 control_rep1|2 95 . 301 control_rep1 4 chr1 -149 550 control_rep1|3 46 . 201 control_rep1 5 chr1 -249 450 control_rep1|5 26 . 101 control_rep1 6 chr1 -49 650 control_rep1|6 25 . 301 control_rep1 7 chr10 -49 650 control_rep1|7 75 . 301 control_rep1 8 chr2 -49 650 control_rep1|8 50 . 301 control_rep1 9 chr4 2 -49 650 control_rep1|10 30 . 301 control_rep1 10 chr4-2 -149 550 control_rep1|11 20 . 201 control_rep1 # ℹ 41 more rows ✔ Genomic regions were successfully centered and expanded. ℹ Argument `trim_start` is set to "TRUE". ℹ Atgument `genome` is set to NA. → Trimming start coordinates of resulting genomic regions. ℹ Some newly-defined genomic regions have a start coordinate below "1". → Values of name for these sites: "control_rep1|1", "control_rep1|2", "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7", "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1", "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5", "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …, "treatment_rep3|5", and "treatment_rep3|8". ✔ These genomic regions were trimmed to get start coordinate "1". ✔ Genomic regions were successfully centered and expanded. ℹ Output format is set to "tibble". → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `outputFormat` is set to "tibble". → The argument `includeByChromosomeName` is a class <character> of length 4 and will be used to retain matchhing chromsome names in chrom. ✔ Entries in chrom with the values "chr1", "chr10", "chr2", and "chr42" are retained. ℹ The following 5 entries in column chrom from the input data were not retained: "Chr2", "chr4 2", "chr4-2", "chr4|2", and "chr4?2". ✔ Input data was filtered to retain regions on defined chromosome. ℹ The argument `excludeByBlacklist` is "NULL". ✔ No filtering by blacklisted regions is done. ℹ The argument `includeAboveScoreCutoff` is "NULL". ✔ No filtering by score threshold is done. ℹ The argument `includeTopNScoring` is "NULL". ✔ No top enriched regions were selected. All input regions are retained. ✔ Filtered dataset will be returned. ℹ Output format is set to "tibble". → Start with the disjoining and filtering genomic regions. ✔ Disjoin and filter by `foundInSamples` of genomic regions successfully finished. → Start with combining remaining genomic regions. ✔ Combining remaining genomic regions was successfully finished. → Start with identification of overlaps between the original summit and remaining genomic regions. ℹ Remaining regions without overlap will be removed. Joining with `by = join_by(ranking)` ✔ Retained genomic regions with input data summit overlap was successfully finished. → Information from input center will be added to output data frame. ℹ Argument `combinedCenter` was defined as "nearest". ℹ The mean of all input centers is calculated and the nearest input center is used → Center information in center and score are added to the output data frame. ✔ Output data frame columns center and score were successfully populated. → The value "combined" for column sample_name was provided. ℹ Column sample_name is filled with provided value combined. ℹ Column name is created as unique identifier for each row containing sample_name and the row number. ✔ The columns sample_name and name were successfully populated. ℹ Argument `annotateWithInputNames` was set to "TRUE". → Column input_names is added to output data frame. ✔ Additional column input_names was successfully populated. ✔ All required columns in output data frame were successfully populated. > Information from input center will be added to output data frame. i Argument `combinedCenter` was defined as "strongest". i Based on column score the strongest input center is idenfied. > Center information in center and score are added to the output data frame. v Output data frame columns center and score were successfully populated. > No value for column sample_name was provided. i Column sample_name is filled with all input sample_names. i Column name is created as unique identifier for each row containing sample_name and the row number. v The columns sample_name and name were successfully populated. i Argument `annotateWithInputNames` was set to "FALSE". v Column input_names is not added to output data frame. v All required columns in output data frame were successfully populated. > Information from input center will be added to output data frame. i Argument `combinedCenter` was defined as "middle". i The middle between start and end and the mean score is calculated. > Newly calculated center information are added to center and score in the output data frame. v Output data frame columns center and score were successfully populated. > No value for column sample_name was provided. i Column sample_name is filled with all input sample_names. i Column name is created as unique identifier for each row containing sample_name and the row number. v The columns sample_name and name were successfully populated. i Argument `annotateWithInputNames` was set to "FALSE". v Column input_names is not added to output data frame. v All required columns in output data frame were successfully populated. > Information from input center will be added to output data frame. i Argument `combinedCenter` was defined as "nearest". i The mean of all input centers is calculated and the nearest input center is used > Center information in center and score are added to the output data frame. v Output data frame columns center and score were successfully populated. > No value for column sample_name was provided. i Column sample_name is filled with all input sample_names. i Column name is created as unique identifier for each row containing sample_name and the row number. v The columns sample_name and name were successfully populated. i Argument `annotateWithInputNames` was set to "FALSE". v Column input_names is not added to output data frame. v All required columns in output data frame were successfully populated. > Information from input center will be added to output data frame. i Argument `combinedCenter` was defined as "strongest". i Based on column score the strongest input center is idenfied. > Center information in center and score are added to the output data frame. v Output data frame columns center and score were successfully populated. > No value for column sample_name was provided. i Column sample_name is filled with all input sample_names. i Column name is created as unique identifier for each row containing sample_name and the row number. v The columns sample_name and name were successfully populated. i Argument `annotateWithInputNames` was set to "FALSE". v Column input_names is not added to output data frame. v All required columns in output data frame were successfully populated. > Information from input center will be added to output data frame. i Argument `combinedCenter` was defined as "middle". i The middle between start and end and the mean score is calculated. > Newly calculated center information are added to center and score in the output data frame. v Output data frame columns center and score were successfully populated. > No value for column sample_name was provided. i Column sample_name is filled with all input sample_names. i Column name is created as unique identifier for each row containing sample_name and the row number. v The columns sample_name and name were successfully populated. i Argument `annotateWithInputNames` was set to "FALSE". v Column input_names is not added to output data frame. v All required columns in output data frame were successfully populated. ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. ✔ `expandBy` was calculated from the input data and set to "350". ℹ Genomic regions will be expanded by 350bp in both direction. ℹ Argument `outputFormat` is set to "tibble". ℹ Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). ℹ Argument `genome` set to NA. ℹ Only start will be trimmed. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `trim_start` is TRUE. → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. → Starting with expanding genomic regions from the column center. → Genomic regions will be centered and expanded. ℹ Used genome for trimming is NA. → Expanding genomic regions from the column center by 350 before and 350 after the center. # A tibble: 51 × 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 251 950 control_rep1|9 80 . 601 control_rep1 2 chr1 -49 650 control_rep1|1 96 . 301 control_rep1 3 chr1 -49 650 control_rep1|2 95 . 301 control_rep1 4 chr1 -149 550 control_rep1|3 46 . 201 control_rep1 5 chr1 -249 450 control_rep1|5 26 . 101 control_rep1 6 chr1 -49 650 control_rep1|6 25 . 301 control_rep1 7 chr10 -49 650 control_rep1|7 75 . 301 control_rep1 8 chr2 -49 650 control_rep1|8 50 . 301 control_rep1 9 chr4 2 -49 650 control_rep1|10 30 . 301 control_rep1 10 chr4-2 -149 550 control_rep1|11 20 . 201 control_rep1 # ℹ 41 more rows ✔ Genomic regions were successfully centered and expanded. ℹ Argument `trim_start` is set to "TRUE". ℹ Atgument `genome` is set to NA. → Trimming start coordinates of resulting genomic regions. ℹ Some newly-defined genomic regions have a start coordinate below "1". → Values of name for these sites: "control_rep1|1", "control_rep1|2", "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7", "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1", "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5", "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …, "treatment_rep3|5", and "treatment_rep3|8". ✔ These genomic regions were trimmed to get start coordinate "1". ✔ Genomic regions were successfully centered and expanded. ℹ Output format is set to "tibble". → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `outputFormat` is set to "tibble". ℹ The argument `includeByChromosomeName` is "NULL". ✔ No filtering for chromosome names in chrom is done. ℹ The argument `excludeByBlacklist` is "NULL". ✔ No filtering by blacklisted regions is done. ℹ The argument `includeAboveScoreCutoff` is "NULL". ✔ No filtering by score threshold is done. ℹ The argument `includeTopNScoring` is "NULL". ✔ No top enriched regions were selected. All input regions are retained. ✔ Filtered dataset will be returned. ℹ Output format is set to "tibble". → Start with the disjoining and filtering genomic regions. ✔ Disjoin and filter by `foundInSamples` of genomic regions successfully finished. > Start with the disjoining and filtering genomic regions. v Disjoin and filter by `foundInSamples` of genomic regions successfully finished. ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. ✔ `expandBy` was calculated from the input data and set to "350". ℹ Genomic regions will be expanded by 350bp in both direction. ℹ Argument `outputFormat` is set to "tibble". ℹ Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). ℹ Argument `genome` set to NA. ℹ Only start will be trimmed. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `trim_start` is TRUE. → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. → Starting with expanding genomic regions from the column center. → Genomic regions will be centered and expanded. ℹ Used genome for trimming is NA. → Expanding genomic regions from the column center by 350 before and 350 after the center. # A tibble: 51 × 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 251 950 control_rep1|9 80 . 601 control_rep1 2 chr1 -49 650 control_rep1|1 96 . 301 control_rep1 3 chr1 -49 650 control_rep1|2 95 . 301 control_rep1 4 chr1 -149 550 control_rep1|3 46 . 201 control_rep1 5 chr1 -249 450 control_rep1|5 26 . 101 control_rep1 6 chr1 -49 650 control_rep1|6 25 . 301 control_rep1 7 chr10 -49 650 control_rep1|7 75 . 301 control_rep1 8 chr2 -49 650 control_rep1|8 50 . 301 control_rep1 9 chr4 2 -49 650 control_rep1|10 30 . 301 control_rep1 10 chr4-2 -149 550 control_rep1|11 20 . 201 control_rep1 # ℹ 41 more rows ✔ Genomic regions were successfully centered and expanded. ℹ Argument `trim_start` is set to "TRUE". ℹ Atgument `genome` is set to NA. → Trimming start coordinates of resulting genomic regions. ℹ Some newly-defined genomic regions have a start coordinate below "1". → Values of name for these sites: "control_rep1|1", "control_rep1|2", "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7", "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1", "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5", "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …, "treatment_rep3|5", and "treatment_rep3|8". ✔ These genomic regions were trimmed to get start coordinate "1". ✔ Genomic regions were successfully centered and expanded. ℹ Output format is set to "tibble". → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `outputFormat` is set to "tibble". → The argument `includeByChromosomeName` is a class <character> of length 4 and will be used to retain matchhing chromsome names in chrom. ✔ Entries in chrom with the values "chr1", "chr10", "chr2", and "chr42" are retained. ℹ The following 5 entries in column chrom from the input data were not retained: "Chr2", "chr4 2", "chr4-2", "chr4|2", and "chr4?2". ✔ Input data was filtered to retain regions on defined chromosome. ℹ The argument `excludeByBlacklist` is "NULL". ✔ No filtering by blacklisted regions is done. ℹ The argument `includeAboveScoreCutoff` is "NULL". ✔ No filtering by score threshold is done. ℹ The argument `includeTopNScoring` is "NULL". ✔ No top enriched regions were selected. All input regions are retained. ✔ Filtered dataset will be returned. ℹ Output format is set to "tibble". → Start with the disjoining and filtering genomic regions. ✔ Disjoin and filter by `foundInSamples` of genomic regions successfully finished. → Start with combining remaining genomic regions. ✔ Combining remaining genomic regions was successfully finished. → Start with identification of overlaps between the original summit and remaining genomic regions. ℹ Remaining regions without overlap will be removed. Joining with `by = join_by(ranking)` ✔ Retained genomic regions with input data summit overlap was successfully finished. → Start with identification of overlaps between the original summit and remaining genomic regions. ℹ Remaining regions without overlap will be removed. Joining with `by = join_by(ranking)` ✔ Retained genomic regions with input data summit overlap was successfully finished. ℹ Regions are not checked for overlap with innput summits. Nothing is removed. ✔ Retained genomic regions with input data summit overlap was successfully finished. ℹ Regions are not checked for overlap with innput summits. Nothing is removed. ✔ Retained genomic regions with input data summit overlap was successfully finished. → Start with identification of overlaps between the original summit and remaining genomic regions. ℹ Remaining regions without overlap will be removed. Joining with `by = join_by(ranking)` ✔ Retained genomic regions with input data summit overlap was successfully finished. ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. ✔ `expandBy` was calculated from the input data and set to "350". ℹ Genomic regions will be expanded by 350bp in both direction. ℹ Argument `outputFormat` is set to "tibble". ℹ Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). ℹ Argument `genome` set to NA. ℹ Only start will be trimmed. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `trim_start` is TRUE. → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. → Starting with expanding genomic regions from the column center. → Genomic regions will be centered and expanded. ℹ Used genome for trimming is NA. → Expanding genomic regions from the column center by 350 before and 350 after the center. # A tibble: 51 × 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 251 950 control_rep1|9 80 . 601 control_rep1 2 chr1 -49 650 control_rep1|1 96 . 301 control_rep1 3 chr1 -49 650 control_rep1|2 95 . 301 control_rep1 4 chr1 -149 550 control_rep1|3 46 . 201 control_rep1 5 chr1 -249 450 control_rep1|5 26 . 101 control_rep1 6 chr1 -49 650 control_rep1|6 25 . 301 control_rep1 7 chr10 -49 650 control_rep1|7 75 . 301 control_rep1 8 chr2 -49 650 control_rep1|8 50 . 301 control_rep1 9 chr4 2 -49 650 control_rep1|10 30 . 301 control_rep1 10 chr4-2 -149 550 control_rep1|11 20 . 201 control_rep1 # ℹ 41 more rows ✔ Genomic regions were successfully centered and expanded. ℹ Argument `trim_start` is set to "TRUE". ℹ Atgument `genome` is set to NA. → Trimming start coordinates of resulting genomic regions. ℹ Some newly-defined genomic regions have a start coordinate below "1". → Values of name for these sites: "control_rep1|1", "control_rep1|2", "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7", "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1", "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5", "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …, "treatment_rep3|5", and "treatment_rep3|8". ✔ These genomic regions were trimmed to get start coordinate "1". ✔ Genomic regions were successfully centered and expanded. ℹ Output format is set to "tibble". → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `outputFormat` is set to "tibble". → The argument `includeByChromosomeName` is a class <character> of length 4 and will be used to retain matchhing chromsome names in chrom. ✔ Entries in chrom with the values "chr1", "chr10", "chr2", and "chr42" are retained. ℹ The following 5 entries in column chrom from the input data were not retained: "Chr2", "chr4 2", "chr4-2", "chr4|2", and "chr4?2". ✔ Input data was filtered to retain regions on defined chromosome. ℹ The argument `excludeByBlacklist` is "NULL". ✔ No filtering by blacklisted regions is done. ℹ The argument `includeAboveScoreCutoff` is "NULL". ✔ No filtering by score threshold is done. ℹ The argument `includeTopNScoring` is "NULL". ✔ No top enriched regions were selected. All input regions are retained. ✔ Filtered dataset will be returned. ℹ Output format is set to "tibble". → Start with the disjoining and filtering genomic regions. ✔ Disjoin and filter by `foundInSamples` of genomic regions successfully finished. → Start with combining remaining genomic regions. ✔ Combining remaining genomic regions was successfully finished. i Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. v `expandBy` was calculated from the input data and set to "350". i Genomic regions will be expanded by 350bp in both direction. ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. ✔ `expandBy` was calculated from the input data and set to "350". ℹ Genomic regions will be expanded by 350bp in both direction. ℹ Argument `outputFormat` is set to "tibble". ℹ Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). ℹ Argument `genome` set to NA. ℹ Only start will be trimmed. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `trim_start` is TRUE. → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. → Starting with expanding genomic regions from the column center. → Genomic regions will be centered and expanded. ℹ Used genome for trimming is NA. → Expanding genomic regions from the column center by 350 before and 350 after the center. # A tibble: 51 × 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 251 950 control_rep1|9 80 . 601 control_rep1 2 chr1 -49 650 control_rep1|1 96 . 301 control_rep1 3 chr1 -49 650 control_rep1|2 95 . 301 control_rep1 4 chr1 -149 550 control_rep1|3 46 . 201 control_rep1 5 chr1 -249 450 control_rep1|5 26 . 101 control_rep1 6 chr1 -49 650 control_rep1|6 25 . 301 control_rep1 7 chr10 -49 650 control_rep1|7 75 . 301 control_rep1 8 chr2 -49 650 control_rep1|8 50 . 301 control_rep1 9 chr4 2 -49 650 control_rep1|10 30 . 301 control_rep1 10 chr4-2 -149 550 control_rep1|11 20 . 201 control_rep1 # ℹ 41 more rows ✔ Genomic regions were successfully centered and expanded. ℹ Argument `trim_start` is set to "TRUE". ℹ Atgument `genome` is set to NA. → Trimming start coordinates of resulting genomic regions. ℹ Some newly-defined genomic regions have a start coordinate below "1". → Values of name for these sites: "control_rep1|1", "control_rep1|2", "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7", "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1", "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5", "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …, "treatment_rep3|5", and "treatment_rep3|8". ✔ These genomic regions were trimmed to get start coordinate "1". ✔ Genomic regions were successfully centered and expanded. ℹ Output format is set to "tibble". → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `outputFormat` is set to "tibble". ℹ The argument `includeByChromosomeName` is "NULL". ✔ No filtering for chromosome names in chrom is done. ℹ The argument `excludeByBlacklist` is "NULL". ✔ No filtering by blacklisted regions is done. ℹ The argument `includeAboveScoreCutoff` is "NULL". ✔ No filtering by score threshold is done. ℹ The argument `includeTopNScoring` is "NULL". ✔ No top enriched regions were selected. All input regions are retained. ✔ Filtered dataset will be returned. ℹ Output format is set to "tibble". ℹ Argument `outputFormat` is set to "tibble". ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. → Start with the disjoining and filtering genomic regions. ✔ Disjoin and filter by `foundInSamples` of genomic regions successfully finished. → Start with combining remaining genomic regions. ✔ Combining remaining genomic regions was successfully finished. → Start with identification of overlaps between the original summit and remaining genomic regions. ℹ Remaining regions without overlap will be removed. Joining with `by = join_by(ranking)` ✔ Retained genomic regions with input data summit overlap was successfully finished. → Information from input center will be added to output data frame. ℹ Argument `combinedCenter` was defined as "nearest". ℹ The mean of all input centers is calculated and the nearest input center is used → Center information in center and score are added to the output data frame. ✔ Output data frame columns center and score were successfully populated. → No value for column sample_name was provided. ℹ Column sample_name is filled with all input sample_names. ℹ Column name is created as unique identifier for each row containing sample_name and the row number. ✔ The columns sample_name and name were successfully populated. ℹ Argument `annotateWithInputNames` was set to "FALSE". ✔ Column input_names is not added to output data frame. ✔ All required columns in output data frame were successfully populated. ✔ Genomic regions were successfully combined. ℹ Output format is set to "tibble". ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. ✔ `expandBy` was calculated from the input data and set to "324". ℹ Genomic regions will be expanded by 324bp in both direction. ℹ Argument `outputFormat` is set to "tibble". ℹ Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). ℹ Argument `genome` set to NA. ℹ Only start will be trimmed. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `trim_start` is TRUE. → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. → Starting with expanding genomic regions from the column center. → Genomic regions will be centered and expanded. ℹ Used genome for trimming is NA. → Expanding genomic regions from the column center by 324 before and 324 after the center. # A tibble: 5 × 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 chr1 -23 624 control_rep1|control_rep2|… 100 . 301 control_re… 2 chr2 -23 624 control_rep1|control_rep2|… 50 . 301 control_re… 3 chr10 -23 624 control_rep1|control_rep2|… 95 . 301 control_re… 4 chr4 2 -23 624 control_rep1|control_rep2|… 35 . 301 control_re… 5 chr4-2 -23 624 control_rep1|control_rep2|… 30 . 301 control_re… ✔ Genomic regions were successfully centered and expanded. ℹ Argument `trim_start` is set to "TRUE". ℹ Atgument `genome` is set to NA. → Trimming start coordinates of resulting genomic regions. ℹ Some newly-defined genomic regions have a start coordinate below "1". → Values of name for these sites: "control_rep1|control_rep2|control_rep3|treatment_rep1|treatment_rep2|treatment_rep3|1", "control_rep1|control_rep2|control_rep3|treatment_rep1|treatment_rep2|treatment_rep3|2", "control_rep1|control_rep2|control_rep3|treatment_rep1|treatment_rep2|treatment_rep3|3", "control_rep1|control_rep2|control_rep3|treatment_rep1|treatment_rep2|treatment_rep3|4", and "control_rep1|control_rep2|control_rep3|treatment_rep1|treatment_rep2|treatment_rep3|5". ✔ These genomic regions were trimmed to get start coordinate "1". ✔ Genomic regions were successfully centered and expanded. ℹ Output format is set to "tibble". > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `outputFormat` is set to "tibble". i The argument `includeByChromosomeName` is "NULL". v No filtering for chromosome names in chrom is done. i The argument `excludeByBlacklist` is "NULL". v No filtering by blacklisted regions is done. i The argument `includeAboveScoreCutoff` is "NULL". v No filtering by score threshold is done. i The argument `includeTopNScoring` is "NULL". v No top enriched regions were selected. All input regions are retained. v Filtered dataset will be returned. i Output format is set to "tibble". > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `outputFormat` is set to "tibble". i The argument `includeByChromosomeName` is "NULL". v No filtering for chromosome names in chrom is done. i The argument `excludeByBlacklist` is "NULL". v No filtering by blacklisted regions is done. i The argument `includeAboveScoreCutoff` is "NULL". v No filtering by score threshold is done. i The argument `includeTopNScoring` is "NULL". v No top enriched regions were selected. All input regions are retained. v Filtered dataset will be returned. i Output format is set to "tibble". > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `outputFormat` is set to "tibble". i The argument `includeByChromosomeName` is "NULL". v No filtering for chromosome names in chrom is done. i The argument `excludeByBlacklist` is "NULL". v No filtering by blacklisted regions is done. i The argument `includeAboveScoreCutoff` is "NULL". v No filtering by score threshold is done. i The argument `includeTopNScoring` is "NULL". v No top enriched regions were selected. All input regions are retained. v Filtered dataset will be returned. i Output format is set to "tibble". > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `outputFormat` is set to "tibble". i The argument `includeByChromosomeName` is "NULL". v No filtering for chromosome names in chrom is done. i The argument `excludeByBlacklist` is "NULL". v No filtering by blacklisted regions is done. i The argument `includeAboveScoreCutoff` is "NULL". v No filtering by score threshold is done. i The argument `includeTopNScoring` is "NULL". v No top enriched regions were selected. All input regions are retained. v Filtered dataset will be returned. i Output format is set to "tibble". > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `outputFormat` is set to "tibble". i The argument `includeByChromosomeName` is "NULL". v No filtering for chromosome names in chrom is done. i The argument `excludeByBlacklist` is "NULL". v No filtering by blacklisted regions is done. i The argument `includeAboveScoreCutoff` is "NULL". v No filtering by score threshold is done. i The argument `includeTopNScoring` is "NULL". v No top enriched regions were selected. All input regions are retained. v Filtered dataset will be returned. i Output format is set to "tibble". > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. i Provide input `data` is a <data.frame> with three or four columns and paths to existing files. > Start loading and preparing data. i Argument `outputFormat` is set to "tibble". i The argument `includeByChromosomeName` is "NULL". v No filtering for chromosome names in chrom is done. i The argument `excludeByBlacklist` is "NULL". v No filtering by blacklisted regions is done. i The argument `includeAboveScoreCutoff` is "NULL". v No filtering by score threshold is done. i The argument `includeTopNScoring` is "NULL". v No top enriched regions were selected. All input regions are retained. v Filtered dataset will be returned. i Output format is set to "tibble". ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. ✔ `expandBy` was calculated from the input data and set to "350". ℹ Genomic regions will be expanded by 350bp in both direction. ℹ Argument `outputFormat` is set to "tibble". ℹ Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). ℹ Argument `genome` set to NA. ℹ Only start will be trimmed. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `trim_start` is TRUE. → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. → Starting with expanding genomic regions from the column center. → Genomic regions will be centered and expanded. ℹ Used genome for trimming is NA. → Expanding genomic regions from the column center by 350 before and 350 after the center. # A tibble: 51 × 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 251 950 control_rep1|9 80 . 601 control_rep1 2 chr1 -49 650 control_rep1|1 96 . 301 control_rep1 3 chr1 -49 650 control_rep1|2 95 . 301 control_rep1 4 chr1 -149 550 control_rep1|3 46 . 201 control_rep1 5 chr1 -249 450 control_rep1|5 26 . 101 control_rep1 6 chr1 -49 650 control_rep1|6 25 . 301 control_rep1 7 chr10 -49 650 control_rep1|7 75 . 301 control_rep1 8 chr2 -49 650 control_rep1|8 50 . 301 control_rep1 9 chr4 2 -49 650 control_rep1|10 30 . 301 control_rep1 10 chr4-2 -149 550 control_rep1|11 20 . 201 control_rep1 # ℹ 41 more rows ✔ Genomic regions were successfully centered and expanded. ℹ Argument `trim_start` is set to "TRUE". ℹ Atgument `genome` is set to NA. → Trimming start coordinates of resulting genomic regions. ℹ Some newly-defined genomic regions have a start coordinate below "1". → Values of name for these sites: "control_rep1|1", "control_rep1|2", "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7", "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1", "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5", "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …, "treatment_rep3|5", and "treatment_rep3|8". ✔ These genomic regions were trimmed to get start coordinate "1". ✔ Genomic regions were successfully centered and expanded. ℹ Output format is set to "tibble". → The argument `includeByChromosomeName` is a class <character> of length 3 and will be used to retain matchhing chromsome names in chrom. ✔ Entries in chrom with the values "chr1", "chr10", and "chr42" are retained. ℹ The following 6 entries in column chrom from the input data were not retained: "Chr2", "chr2", "chr4 2", "chr4-2", "chr4|2", and "chr4?2". ✔ Input data was filtered to retain regions on defined chromosome. → User provied dataframe will be used for blacklist filtering. ! Provided blacklist contains chromosome names (in chrom) not found in input data. ℹ The following blacklist chromosomes have no match: "chr1" and "chr42". → Note to user: Please doublecheck this observation. ✔ Input data was filtered by blacklist. > User provied dataframe will be used for blacklist filtering. ! Provided blacklist contains chromosome names (in chrom) not found in input data. i The following blacklist chromosomes have no match: "chr1" and "chr42". > Note to user: Please doublecheck this observation. v Input data was filtered by blacklist. i The argument `excludeByBlacklist` is "NULL". v No filtering by blacklisted regions is done. i The argument `excludeByBlacklist` is "NULL". v No filtering by blacklisted regions is done. > User provied GenomicRanges object will be used for blacklist filtering. ! Provided blacklist contains chromosome names (in chrom) not found in input data. i The following blacklist chromosomes have no match: "chr1" and "chr42". > Note to user: Please doublecheck this observation. i The argument `excludeByBlacklist` is a class <GRanges>. > Using GenmoicRanges option for filtering. v Input data was filtered by blacklist. > User provied dataframe will be used for blacklist filtering. ! Provided blacklist contains chromosome names (in chrom) not found in input data. i The following blacklist chromosomes have no match: "chr1" and "chr42". > Note to user: Please doublecheck this observation. v Input data was filtered by blacklist. > User provied dataframe will be used for blacklist filtering. ! Provided blacklist contains chromosome names (in chrom) not found in input data. i The following blacklist chromosomes have no match: "chr1" and "chr42". > Note to user: Please doublecheck this observation. v Input data was filtered by blacklist. ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. ✔ `expandBy` was calculated from the input data and set to "350". ℹ Genomic regions will be expanded by 350bp in both direction. ℹ Argument `outputFormat` is set to "tibble". ℹ Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). ℹ Argument `genome` set to NA. ℹ Only start will be trimmed. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `trim_start` is TRUE. → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. → Starting with expanding genomic regions from the column center. → Genomic regions will be centered and expanded. ℹ Used genome for trimming is NA. → Expanding genomic regions from the column center by 350 before and 350 after the center. # A tibble: 51 × 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 251 950 control_rep1|9 80 . 601 control_rep1 2 chr1 -49 650 control_rep1|1 96 . 301 control_rep1 3 chr1 -49 650 control_rep1|2 95 . 301 control_rep1 4 chr1 -149 550 control_rep1|3 46 . 201 control_rep1 5 chr1 -249 450 control_rep1|5 26 . 101 control_rep1 6 chr1 -49 650 control_rep1|6 25 . 301 control_rep1 7 chr10 -49 650 control_rep1|7 75 . 301 control_rep1 8 chr2 -49 650 control_rep1|8 50 . 301 control_rep1 9 chr4 2 -49 650 control_rep1|10 30 . 301 control_rep1 10 chr4-2 -149 550 control_rep1|11 20 . 201 control_rep1 # ℹ 41 more rows ✔ Genomic regions were successfully centered and expanded. ℹ Argument `trim_start` is set to "TRUE". ℹ Atgument `genome` is set to NA. → Trimming start coordinates of resulting genomic regions. ℹ Some newly-defined genomic regions have a start coordinate below "1". → Values of name for these sites: "control_rep1|1", "control_rep1|2", "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7", "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1", "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5", "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …, "treatment_rep3|5", and "treatment_rep3|8". ✔ These genomic regions were trimmed to get start coordinate "1". ✔ Genomic regions were successfully centered and expanded. ℹ Output format is set to "tibble". → The argument `includeByChromosomeName` is a class <character> of length 3 and will be used to retain matchhing chromsome names in chrom. ✔ Entries in chrom with the values "chr1", "chr10", and "chr42" are retained. ℹ The following 6 entries in column chrom from the input data were not retained: "Chr2", "chr2", "chr4 2", "chr4-2", "chr4|2", and "chr4?2". ✔ Input data was filtered to retain regions on defined chromosome. > The argument `includeByChromosomeName` is a class <character> of length 3 and will be used to retain matchhing chromsome names in chrom. v Entries in chrom with the values "chr1", "chr10", and "chr42" are retained. i The following 6 entries in column chrom from the input data were not retained: "Chr2", "chr2", "chr4 2", "chr4-2", "chr4|2", and "chr4?2". v Input data was filtered to retain regions on defined chromosome. i The argument `includeByChromosomeName` is "NULL". v No filtering for chromosome names in chrom is done. > The argument `includeByChromosomeName` is a class <character> of length 1 and will be used to retain matchhing chromsome names in chrom. v Entries in chrom with the value "chr1" are retained. i The following 2 entries in column chrom from the input data were not retained: "chr10" and "chr42". v Input data was filtered to retain regions on defined chromosome. > The argument `includeByChromosomeName` is a class <character> of length 3 and will be used to retain matchhing chromsome names in chrom. v Entries in chrom with the values "chr1", "chr10", and "chr42" are retained. v Input data was filtered to retain regions on defined chromosome. ! `includeByChromosomeName` has the wrong class. > `includeByChromosomeName` is converted to <character>. ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. ✔ `expandBy` was calculated from the input data and set to "350". ℹ Genomic regions will be expanded by 350bp in both direction. ℹ Argument `outputFormat` is set to "tibble". ℹ Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). ℹ Argument `genome` set to NA. ℹ Only start will be trimmed. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `trim_start` is TRUE. → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. → Starting with expanding genomic regions from the column center. → Genomic regions will be centered and expanded. ℹ Used genome for trimming is NA. → Expanding genomic regions from the column center by 350 before and 350 after the center. # A tibble: 51 × 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 251 950 control_rep1|9 80 . 601 control_rep1 2 chr1 -49 650 control_rep1|1 96 . 301 control_rep1 3 chr1 -49 650 control_rep1|2 95 . 301 control_rep1 4 chr1 -149 550 control_rep1|3 46 . 201 control_rep1 5 chr1 -249 450 control_rep1|5 26 . 101 control_rep1 6 chr1 -49 650 control_rep1|6 25 . 301 control_rep1 7 chr10 -49 650 control_rep1|7 75 . 301 control_rep1 8 chr2 -49 650 control_rep1|8 50 . 301 control_rep1 9 chr4 2 -49 650 control_rep1|10 30 . 301 control_rep1 10 chr4-2 -149 550 control_rep1|11 20 . 201 control_rep1 # ℹ 41 more rows ✔ Genomic regions were successfully centered and expanded. ℹ Argument `trim_start` is set to "TRUE". ℹ Atgument `genome` is set to NA. → Trimming start coordinates of resulting genomic regions. ℹ Some newly-defined genomic regions have a start coordinate below "1". → Values of name for these sites: "control_rep1|1", "control_rep1|2", "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7", "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1", "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5", "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …, "treatment_rep3|5", and "treatment_rep3|8". ✔ These genomic regions were trimmed to get start coordinate "1". ✔ Genomic regions were successfully centered and expanded. ℹ Output format is set to "tibble". → Significance in score is filtered and all regions above 40 will be retained. ℹ A total of 37 of 51 input regions are retained with value in score a above 40. ✔ Input data was filtered to retain regions with a score above the defined threshold. > Significance in score is filtered and all regions above 0.01 will be retained. i A total of 51 of 51 input regions are retained with value in score a above 0.01. v Input data was filtered to retain regions with a score above the defined threshold. i The argument `includeAboveScoreCutoff` is "NULL". v No filtering by score threshold is done. > Significance in score is filtered and all regions above 0 will be retained. i A total of 37 of 37 input regions are retained with value in score a above 0. v Input data was filtered to retain regions with a score above the defined threshold. ℹ Input value for `expandBy` is "NULL". Median of all input genomic regions is calculated and returned for expansion. ✔ `expandBy` was calculated from the input data and set to "350". ℹ Genomic regions will be expanded by 350bp in both direction. ℹ Argument `outputFormat` is set to "tibble". ℹ Input data `data` has no assigned genome. ! Input data `data` has no assigned genome (NA). ℹ Argument `genome` set to NA. ℹ Only start will be trimmed. ℹ Provide input `data` is a <data.frame> with three or four columns and paths to existing files. → Start loading and preparing data. ℹ Argument `trim_start` is TRUE. → Checking <class> and "values" of all columns. ✔ Structure of data was successfully checked to be an accepted input. → Starting with expanding genomic regions from the column center. → Genomic regions will be centered and expanded. ℹ Used genome for trimming is NA. → Expanding genomic regions from the column center by 350 before and 350 after the center. # A tibble: 51 × 8 chrom start end name score strand center sample_name <chr> <int> <int> <chr> <dbl> <chr> <dbl> <chr> 1 Chr2 251 950 control_rep1|9 80 . 601 control_rep1 2 chr1 -49 650 control_rep1|1 96 . 301 control_rep1 3 chr1 -49 650 control_rep1|2 95 . 301 control_rep1 4 chr1 -149 550 control_rep1|3 46 . 201 control_rep1 5 chr1 -249 450 control_rep1|5 26 . 101 control_rep1 6 chr1 -49 650 control_rep1|6 25 . 301 control_rep1 7 chr10 -49 650 control_rep1|7 75 . 301 control_rep1 8 chr2 -49 650 control_rep1|8 50 . 301 control_rep1 9 chr4 2 -49 650 control_rep1|10 30 . 301 control_rep1 10 chr4-2 -149 550 control_rep1|11 20 . 201 control_rep1 # ℹ 41 more rows ✔ Genomic regions were successfully centered and expanded. ℹ Argument `trim_start` is set to "TRUE". ℹ Atgument `genome` is set to NA. → Trimming start coordinates of resulting genomic regions. ℹ Some newly-defined genomic regions have a start coordinate below "1". → Values of name for these sites: "control_rep1|1", "control_rep1|2", "control_rep1|3", "control_rep1|5", "control_rep1|6", "control_rep1|7", "control_rep1|8", "control_rep1|10", "control_rep1|11", "control_rep2|1", "control_rep2|2", "control_rep2|3", "control_rep2|4", "control_rep2|5", "control_rep2|6", "control_rep2|7", "control_rep2|8", "control_rep2|9", …, "treatment_rep3|5", and "treatment_rep3|8". ✔ These genomic regions were trimmed to get start coordinate "1". ✔ Genomic regions were successfully centered and expanded. ℹ Output format is set to "tibble". ℹ The argument `includeTopNScoring` extracted the the top 10 regions by score per sample (based on the values in sample_name). → The top enriched 10 regions per sample will be retained. ℹ The argument `includeTopNScoring` was defined as 10. → The following "sample_names" contain less regions then defined by `includeTopNScoring`: control_rep2, control_rep3, treatment_rep1, treatment_rep2, and treatment_rep3 ! No genomic regions will be removed for such samples. ✔ Input data was filtered and the top 10 enriched regions per sample are retained. i The argument `includeTopNScoring` extracted the the top 10 regions by score per sample (based on the values in sample_name). > The top enriched 10 regions per sample will be retained. i The argument `includeTopNScoring` was defined as 10. > The following "sample_names" contain less regions then defined by `includeTopNScoring`: control_rep2, control_rep3, treatment_rep1, treatment_rep2, and treatment_rep3 ! No genomic regions will be removed for such samples. v Input data was filtered and the top 10 enriched regions per sample are retained. i The argument `includeTopNScoring` is "NULL". v No top enriched regions were selected. All input regions are retained. i The argument `includeTopNScoring` extracted the the top 5 regions by score per sample (based on the values in sample_name). > The top enriched 5 regions per sample will be retained. v Input data was filtered and the top 5 enriched regions per sample are retained. i Argument `outputFormat` is set to "GenomicRanges". i Argument `startsAreBased` is 1. i Argument `starts.in.df.are.0based` is FALSE. i Provide input `data` is a pre-loaded <data.frame> with the required column names. > Start preparing data. i Required columns will be added if missing. ! Column 'name' from `data` will be overwritten. > Column 'name' is a computed column from peakCombiner and therefore pre-exisiting data in a column 'name' will not be retained. ! Column 'center' does exist in `data_prepared`. > The column 'center' is taken to define output column 'center'. > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. > Checking whether duplicated regions exist and need to be collapsed. > Checked whether duplicated regions exist and need to be collapsed. v Duplicated regions identified and collapsed to unique chrom, start, and end for each sample by strongest score value. v Preparation of data finished successfully. i Output format is set to "GenomicRanges". i No input genome annotation assigned to ouutput. > Checking <class> and "values" of all columns. v Structure of data was successfully checked to be an accepted input. [ FAIL 0 | WARN 1 | SKIP 0 | PASS 479 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 479 ] > > proc.time() user system elapsed 44.568 1.040 45.613
peakCombiner.Rcheck/peakCombiner-Ex.timings
name | user | system | elapsed | |
centerExpandRegions | 3.679 | 0.152 | 3.832 | |
combineRegions | 1.185 | 0.006 | 1.191 | |
filterRegions | 0.641 | 0.120 | 0.761 | |
prepareInputRegions | 0.575 | 0.031 | 0.607 | |