Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-16 11:38 -0400 (Tue, 16 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4677 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4416 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4444 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4393 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4373 |
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 436/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
COTAN 2.5.6 (landing page) Galfrè Silvia Giulia
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the COTAN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COTAN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: COTAN |
Version: 2.5.6 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings COTAN_2.5.6.tar.gz |
StartedAt: 2024-07-15 21:47:04 -0400 (Mon, 15 Jul 2024) |
EndedAt: 2024-07-15 22:07:26 -0400 (Mon, 15 Jul 2024) |
EllapsedTime: 1222.1 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: COTAN.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings COTAN_2.5.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/COTAN.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘COTAN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘COTAN’ version ‘2.5.6’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘COTAN’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘torch’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Unexported object imported by a ':::' call: ‘ggplot2:::ggname’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GDIPlot: no visible binding for global variable ‘sum.raw.norm’ GDIPlot: no visible binding for global variable ‘GDI’ UMAPPlot: no visible binding for global variable ‘x’ UMAPPlot: no visible binding for global variable ‘y’ UMAPPlot: no visible binding for global variable ‘types’ calculateCoex_Legacy: no visible binding for global variable ‘expectedNN’ calculateCoex_Legacy: no visible binding for global variable ‘expectedNY’ calculateCoex_Legacy: no visible binding for global variable ‘expectedYN’ calculateCoex_Legacy: no visible binding for global variable ‘expectedYY’ calculateCoex_Legacy: no visible binding for global variable ‘observedYY’ calculateCoex_Legacy: no visible binding for global variable ‘.’ calculateG: no visible binding for global variable ‘observedNN’ calculateG: no visible binding for global variable ‘observedNY’ calculateG: no visible binding for global variable ‘observedYN’ calculateG: no visible binding for global variable ‘observedYY’ calculateG: no visible binding for global variable ‘expectedNN’ calculateG: no visible binding for global variable ‘expectedNY’ calculateG: no visible binding for global variable ‘expectedYN’ calculateG: no visible binding for global variable ‘expectedYY’ calculatePartialCoex: no visible binding for global variable ‘expectedNN’ calculatePartialCoex: no visible binding for global variable ‘expectedNY’ calculatePartialCoex: no visible binding for global variable ‘expectedYN’ calculatePartialCoex: no visible binding for global variable ‘expectedYY’ calculatePartialCoex: no visible binding for global variable ‘observedYY’ calculatePartialCoex: no visible binding for global variable ‘.’ cellsUniformClustering: no visible binding for global variable ‘objSeurat’ cellsUniformClustering: no visible binding for global variable ‘usedMaxResolution’ cellsUniformClustering: no visible binding for global variable ‘permMap’ checkClusterUniformity: ... may be used in an incorrect context: ‘c(..., nuPlot, zoomedNuPlot)’ checkClusterUniformity: no visible binding for global variable ‘nuPlot’ checkClusterUniformity: no visible binding for global variable ‘zoomedNuPlot’ cleanPlots: no visible binding for global variable ‘PC1’ cleanPlots: no visible binding for global variable ‘PC2’ cleanPlots: no visible binding for global variable ‘n’ cleanPlots: no visible binding for global variable ‘means’ cleanPlots: no visible binding for global variable ‘nu’ clustersMarkersHeatmapPlot: no visible binding for global variable ‘condName’ clustersMarkersHeatmapPlot: no visible binding for global variable ‘conditions’ clustersSummaryPlot: no visible binding for global variable ‘keys’ clustersSummaryPlot: no visible binding for global variable ‘values’ clustersSummaryPlot: no visible binding for global variable ‘CellNumber’ clustersSummaryPlot: no visible binding for global variable ‘ExpGenes’ clustersSummaryPlot: no visible binding for global variable ‘Cluster’ clustersSummaryPlot: no visible binding for global variable ‘Condition’ establishGenesClusters: no visible binding for global variable ‘secondaryMarkers’ establishGenesClusters: no visible binding for global variable ‘GCS’ establishGenesClusters: no visible binding for global variable ‘rankGenes’ expectedContingencyTables: no visible binding for global variable ‘expectedN’ expectedPartialContingencyTables: no visible binding for global variable ‘expectedNN’ expectedPartialContingencyTables: no visible binding for global variable ‘expectedN’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘group’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘y’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘x’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘width’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘violinwidth’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘xmax’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘xminv’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘xmaxv’ heatmapPlot: no visible binding for global variable ‘obj’ heatmapPlot: no visible binding for global variable ‘type’ heatmapPlot: no visible binding for global variable ‘g2’ heatmapPlot: no visible binding for global variable ‘coex’ mergeUniformCellsClusters : testPairListMerge: no visible binding for global variable ‘cl1’ mergeUniformCellsClusters : testPairListMerge: no visible binding for global variable ‘cl2’ mergeUniformCellsClusters : testPairListMerge : <anonymous>: no visible binding for global variable ‘cl1’ mergeUniformCellsClusters : testPairListMerge : <anonymous>: no visible binding for global variable ‘cl2’ mergeUniformCellsClusters: no visible binding for global variable ‘permMap’ mitochondrialPercentagePlot: no visible binding for global variable ‘mit.percentage’ observedContingencyTables: no visible binding for global variable ‘observedY’ observedPartialContingencyTables: no visible binding for global variable ‘observedYY’ observedPartialContingencyTables: no visible binding for global variable ‘observedY’ scatterPlot: no visible binding for global variable ‘.x’ calculateCoex,COTAN: no visible binding for global variable ‘useTorch’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘rawNorm’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘nu’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘lambda’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘a’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘hk’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘clusters’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘clusterData’ Undefined global functions or variables: . .x CellNumber Cluster Condition ExpGenes GCS GDI PC1 PC2 a cl1 cl2 clusterData clusters coex condName conditions expectedN expectedNN expectedNY expectedYN expectedYY g2 group hk keys lambda means mit.percentage n nu nuPlot obj objSeurat observedNN observedNY observedY observedYN observedYY permMap rankGenes rawNorm secondaryMarkers sum.raw.norm type types useTorch usedMaxResolution values violinwidth width x xmax xmaxv xminv y zoomedNuPlot * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed UniformClusters 189.885 0.899 188.343 CalculatingCOEX 54.522 1.585 54.708 HeatmapPlots 33.610 0.725 33.329 HandlingClusterizations 30.237 0.566 30.705 ParametersEstimations 24.326 0.227 24.533 GenesStatistics 10.862 0.201 10.704 COTANObjectCreation 8.759 0.256 8.700 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘outputTestDatasetCreation.R’ Running ‘spelling.R’ Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... ERROR Error(s) in re-building vignettes: ... --- re-building ‘Guided_tutorial_v2.Rmd’ using rmarkdown Quitting from lines 48-64 [unnamed-chunk-3] (Guided_tutorial_v2.Rmd) Error: processing vignette 'Guided_tutorial_v2.Rmd' failed with diagnostics: cannot open the connection --- failed re-building ‘Guided_tutorial_v2.Rmd’ SUMMARY: processing the following file failed: ‘Guided_tutorial_v2.Rmd’ Error: Vignette re-building failed. Execution halted * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/COTAN.Rcheck/00check.log’ for details.
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘COTAN’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: ... may be used in an incorrect context ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (COTAN)
COTAN.Rcheck/tests/outputTestDatasetCreation.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > # Creates the files to be reloaded by the tests for comparisons > library(zeallot) > > outputTestDatasetCreation <- function(testsDir = file.path("tests", + "testthat")) { + utils::data("test.dataset", package = "COTAN") + options(parallelly.fork.enable = TRUE) + + obj <- COTAN(raw = test.dataset) + obj <- initializeMetaDataset(obj, GEO = " ", + sequencingMethod = "artificial", + sampleCondition = "test") + + obj <- proceedToCoex(obj, cores = 6L, saveObj = FALSE) + #saveRDS(obj, file = file.path(testsDir,"temp.RDS")) + + cells.names.test <- getCells(obj)[c(1L:10L, 591L:610L, 991L:1000L)] + genes.names.test <- getGenes(obj)[c(1L:10L, 291L:310L, 591L: 600L)] + saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS")) + saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS")) + + dispersion.test <- getDispersion(obj)[genes.names.test] + saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS")) + + raw.norm.test <- getNuNormData(obj)[genes.names.test, cells.names.test] + saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS")) + + coex.test <- getGenesCoex(obj, genes = genes.names.test, zeroDiagonal = FALSE) + saveRDS(coex.test, file.path(testsDir, "coex.test.RDS")) + + lambda.test <- getLambda(obj)[genes.names.test] + saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS")) + + GDI.test <- calculateGDI(obj) + GDI.test <- GDI.test[genes.names.test, ] + saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS")) + + nu.test <- getNu(obj)[cells.names.test] + saveRDS(nu.test, file.path(testsDir, "nu.test.RDS")) + + pval.test <- calculatePValue(obj, geneSubsetCol = genes.names.test) + saveRDS(pval.test, file.path(testsDir, "pval.test.RDS")) + + GDIThreshold <- 1.46 + ratioAboveThreshold <- 0.01 + initialResolution <- 0.8 + clusters <- cellsUniformClustering(obj, GDIThreshold = GDIThreshold, + ratioAboveThreshold = ratioAboveThreshold, + initialResolution = initialResolution, + cores = 6L, saveObj = FALSE)[["clusters"]] + saveRDS(clusters, file.path(testsDir, "clusters1.RDS")) + + coexDF <- DEAOnClusters(obj, clusters = clusters) + obj <- addClusterization(obj, clName = "clusters", + clusters = clusters, coexDF = coexDF) + + saveRDS(coexDF[genes.names.test, ], + file.path(testsDir, "coex.test.cluster1.RDS")) + + pvalDF <- pValueFromDEA(coexDF, getNumCells(obj), adjustmentMethod = "none") + + saveRDS(pvalDF[genes.names.test, ], + file.path(testsDir, "pval.test.cluster1.RDS")) + + c(mergedClusters, mCoexDF) %<-% + mergeUniformCellsClusters(objCOTAN = obj, + clusters = NULL, + GDIThreshold = GDIThreshold, + cores = 6L, + distance = "cosine", + hclustMethod = "ward.D2", + saveObj = FALSE) + + saveRDS(mergedClusters[genes.names.test], + file.path(testsDir, "cluster_data_merged.RDS")) + } > > proc.time() user system elapsed 0.175 0.027 0.192
COTAN.Rcheck/tests/spelling.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > if (requireNamespace("spelling", quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.161 0.025 0.175
COTAN.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > Sys.setenv(R_TESTS = "") > library(testthat) > library(COTAN) > test_check("COTAN") Setting new log level to 4 Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10 Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.26952290534973 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00109696388244629 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00612473487854004 Estimating genes' coex Calculate genes' coex elapsed time: 0.862724304199219 Total calculations elapsed time: 3.13946890830994 Calculate genes' coex (legacy): DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate dispersion: START Effective number of cores used: 1 Executing 4 genes batches from [1:2] to [7:8] Executing 1 genes batches from [9:10] to [9:10] Estimate dispersion: DONE dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 4 cells batches from [1:3] to [10:11] Executing 3 cells batches from [12:14] to [18:20] Estimate nu: DONE nu change (abs) | max: 1.75595238095238 | median: 1.07174634176587 | mean: 1.07174634176587 Estimate 'dispersion'/'nu': START Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 1.0362548828125 | max: 4.60986328125 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.0265938895089288 | median: 0.0144680038331048 | mean: 0.0144680038331048 Nu mean: 1.69633192486233 Marginal errors | max: 1.95570586131367 | median 1.32068160171502 | mean: 1.33375826507259 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.058837890625 | max: 3.528076171875 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.416683423613994 | median: 0.239880630367975 | mean: 0.239880630367975 Nu mean: 0.823197206753982 Marginal errors | max: 0.836359531101206 | median 0.703684202571891 | mean: 0.645537958989614 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.32879638671875 | max: 4.0302734375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.164237872898673 | median: 0.0955985184389135 | mean: 0.0955985184389135 Nu mean: 1.06863935445976 Marginal errors | max: 0.259872988828242 | median 0.213703042752633 | mean: 0.197386407582083 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.2294921875 | max: 3.8720703125 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.055185575120883 | median: 0.0319991762044448 | mean: 0.0319991762044448 Nu mean: 0.976813601083562 Marginal errors | max: 0.0951586919577032 | median 0.079429703709466 | mean: 0.0724140148396648 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.2637939453125 | max: 3.929443359375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.0196211148938294 | median: 0.01138609597457 | mean: 0.01138609597457 Nu mean: 1.00823501891926 Marginal errors | max: 0.0327747321002292 | median 0.0272104747849538 | mean: 0.0248963830312038 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.25177001953125 | max: 3.90966796875 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.00670099066960717 | median: 0.00388888266671264 | mean: 0.00388888266671264 Nu mean: 0.997187891997105 Marginal errors | max: 0.0114324509186883 | median 0.0094232649770607 | mean: 0.00863113610779571 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.25592041015625 | max: 3.91650390625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.00230093811689414 | median: 0.00132529122122246 | mean: 0.00132529122122246 Nu mean: 1.00097564689567 Marginal errors | max: 0.00387133150664631 | median 0.0031091017608853 | mean: 0.00286071175800213 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.2545166015625 | max: 3.914306640625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.000837011646904529 | median: 0.000470837393363011 | mean: 0.000470837393363011 Nu mean: 0.999633825746458 Marginal errors | max: 0.00122501723202006 | median 0.00102126435760308 | mean: 0.000943992659051318 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.000209227351122054 | median: 0.000122070312500028 | mean: 0.000122070312500028 Nu mean: 1.00008715703862 Marginal errors | max: 0.000364602956581805 | median 0.000313956936819793 | mean: 0.000282899574318485 Estimate dispersion/nu: DONE Estimate 'dispersion'/'nu': START Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10 While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.27478408813477 Calculating genes' coex normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000691890716552734 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00301814079284668 Estimating genes' coex Calculate genes' coex elapsed time: 0.863190174102783 Total calculations elapsed time: 3.14168429374695 Calculate genes' coex (legacy): DONE Calculate cells' coex (legacy): START Retrieving expected cells' contingency table calculating NN.. done calculating YN..NY..YY..t().. done Expected cells' contingency table elapsed time: 2.22438669204712 Calculating cells' coex normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.000706195831298828 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00225996971130371 Estimating cells' coex Calculate cells' coex elapsed time: 0.750348567962646 Total calculations elapsed time: 2.97770142555237 Calculate cells' coex (legacy): DONE Initializing `COTAN` meta-data Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate 'dispersion'/'nu': START Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.903564453125 | max: 4.679443359375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014 Nu mean: 1.68489292689732 Marginal errors | max: 1.73564890252257 | median 1.37996360874076 | mean: 1.32180348113228 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.0655517578125 | max: 3.5439453125 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.402649984216273 | median: 0.231868788425666 | mean: 0.231868788425666 Nu mean: 0.829218804209393 Marginal errors | max: 0.80321315986594 | median 0.677497553540581 | mean: 0.619375430892821 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.3260498046875 | max: 4.026123046875 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.158004893526231 | median: 0.0919692884670312 | mean: 0.0919692884670312 Nu mean: 1.0660356050592 Marginal errors | max: 0.250724014302326 | median 0.206232152124436 | mean: 0.190425623677198 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.23040771484375 | max: 3.8736572265625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.0532774732102337 | median: 0.0308837890624999 | mean: 0.0308837890624999 Nu mean: 0.977606315852266 Marginal errors | max: 0.0916983669060123 | median 0.0765266929824948 | mean: 0.0697593208689684 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.26348876953125 | max: 3.928955078125 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.0189966206463044 | median: 0.0110199320575908 | mean: 0.0110199320575908 Nu mean: 1.00797668858871 Marginal errors | max: 0.0317151207459254 | median 0.0262702142278251 | mean: 0.0240886952086962 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.2518310546875 | max: 3.9097900390625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.00670088501353994 | median: 0.00388888101583662 | mean: 0.00388888101583662 Nu mean: 0.997187996002297 Marginal errors | max: 0.0113693316356223 | median 0.00939669372836249 | mean: 0.00860715734056932 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.2559814453125 | max: 3.9166259765625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.00251007446998996 | median: 0.00144735987374958 | mean: 0.00144735987374958 Nu mean: 1.00106271459624 Marginal errors | max: 0.00406746973787442 | median 0.00343393462175534 | mean: 0.00313496757119527 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.25445556640625 | max: 3.9140625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.000837027590858019 | median: 0.000488281249999889 | mean: 0.000488281249999889 Nu mean: 0.999651253659142 Marginal errors | max: 0.00143433714371533 | median 0.00116636244706747 | mean: 0.00109289166947839 Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 1 cells batches from [1:20] to [1:20] Estimate nu: DONE nu change (abs) | max: 0.000209227688885871 | median: 0.0001220703125 | mean: 0.0001220703125 Nu mean: 1.00008715737639 Marginal errors | max: 0.000379524846207957 | median 0.000325685250686547 | mean: 0.000295532844332236 Estimate dispersion/nu: DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.28055143356323 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000514984130859375 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00141191482543945 Estimating genes' coex Calculate genes' coex elapsed time: 0.728862285614014 Total calculations elapsed time: 3.01134061813354 Calculate genes' coex (legacy): DONE Calculate cells' coex (legacy): START Retrieving expected cells' contingency table calculating NN.. done calculating YN..NY..YY..t().. done Expected cells' contingency table elapsed time: 2.33336234092712 Calculating cells' coex normalization factor Calculate cells' normalization factor elapsed time: 0.000553131103515625 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00147771835327148 Estimating cells' coex Calculate cells' coex elapsed time: 0.782799482345581 Total calculations elapsed time: 3.11819267272949 Calculate cells' coex (legacy): DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE Calculate genes' partial coex: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial coex normalization factor Fraction of genes with very low expected contingency tables: 0.325 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial coex Calculate genes' partial coex: DONE Calculate cells' partial coex: START Retrieving expected cells' partial contingency table calculating partial NN.. done calculating partial YN..NY..YY.. done Calculating cells' partial coex normalization factor Fraction of genes with very low expected contingency tables: 0 Retrieving observed cells' yes/yes partial contingency table calculating partial YY.. done Estimating cells' partial coex Calculate cells' partial coex: DONE Asked to drop 2 genes and 0 cells Asked to drop 0 genes and 4 cells Asked to drop 2 genes and 2 cells Attaching package: 'rlang' The following objects are masked from 'package:testthat': is_false, is_null, is_true Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells calculating YY.. done calculating YY.. done calculating YN..NY..NN..t().. done Estimate dispersion: START Effective number of cores used: 1 Executing 3 genes batches from [1:3] to [8:10] Estimate dispersion: DONE dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10 calculating NN.. done calculating NN.. done calculating NY..YN..YY..t().. done Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.16419863700867 Calculating genes' coex normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000654458999633789 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00142288208007812 Estimating genes' coex Calculate genes' coex elapsed time: 0.736881971359253 Total calculations elapsed time: 2.90315794944763 Calculate genes' coex (legacy): DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.44300127029419 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000520944595336914 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00148105621337891 Estimating genes' coex Calculate genes' coex elapsed time: 0.768895864486694 Total calculations elapsed time: 3.2138991355896 Calculate genes' coex (legacy): DONE Calculate genes' partial coex: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial coex normalization factor Fraction of genes with very low expected contingency tables: 0.1 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial coex Calculate genes' partial coex: DONE Calculate genes' partial coex: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial coex normalization factor Fraction of genes with very low expected contingency tables: 0.4 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial coex Calculate genes' partial coex: DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells calculating YY.. done calculating YY.. done calculating NY..YN..NN..t().. done Estimate 'dispersion'/'nu': START Estimate dispersion: START Effective number of cores used: 1 Executing 3 genes batches from [1:3] to [8:10] Estimate dispersion: DONE dispersion | min: 0.903564453125 | max: 4.679443359375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 4 cells batches from [1:4] to [13:16] Executing 1 cells batches from [17:20] to [17:20] Estimate nu: DONE nu change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014 Nu mean: 1.68489292689732 Marginal errors | max: 0.25535328937316 | median 0.0807577993228135 | mean: 0.101980750205762 Estimate dispersion: START Effective number of cores used: 1 Executing 3 genes batches from [1:3] to [8:10] Estimate dispersion: DONE dispersion | min: 1.037109375 | max: 4.6107177734375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 4 cells batches from [1:4] to [13:16] Executing 1 cells batches from [17:20] to [17:20] Estimate nu: DONE nu change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011 Nu mean: 1.69735147626627 Marginal errors | max: 0.00326864580272002 | median 0.00111524657842743 | mean: 0.00131556083122533 Estimate dispersion: START Effective number of cores used: 1 Executing 3 genes batches from [1:3] to [8:10] Estimate dispersion: DONE dispersion | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 4 cells batches from [1:4] to [13:16] Executing 1 cells batches from [17:20] to [17:20] Estimate nu: DONE nu change (abs) | max: 0 | median: 0 | mean: 0 Nu mean: 1.69735147626627 Marginal errors | max: 7.56328383637594e-05 | median 1.72948087246994e-05 | mean: 2.99252342145451e-05 Estimate dispersion/nu: DONE calculating NN.. done calculating NN.. done calculating YN..NY..YY..t().. done Calculate cells' coex (legacy): START Retrieving expected cells' contingency table calculating NN.. done calculating YN..NY..YY..t().. done Expected cells' contingency table elapsed time: 2.19077277183533 Calculating cells' coex normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.000659465789794922 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00145816802978516 Estimating cells' coex Calculate cells' coex elapsed time: 0.727115869522095 Total calculations elapsed time: 2.920006275177 Calculate cells' coex (legacy): DONE Calculate cells' partial coex: START Retrieving expected cells' partial contingency table calculating partial NN.. done calculating partial YN..NY..YY.. done Calculating cells' partial coex normalization factor Fraction of genes with very low expected contingency tables: 0 Retrieving observed cells' yes/yes partial contingency table calculating partial YY.. done Estimating cells' partial coex Calculate cells' partial coex: DONE Calculate cells' partial coex: START Retrieving expected cells' partial contingency table calculating partial NN.. done calculating partial YN..NY..YY.. done Calculating cells' partial coex normalization factor Fraction of genes with very low expected contingency tables: 0 Retrieving observed cells' yes/yes partial contingency table calculating partial YY.. done Estimating cells' partial coex Calculate cells' partial coex: DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate 'dispersion'/'nu': START Estimate dispersion: START Effective number of cores used: 1 Executing 3 genes batches from [1:3] to [8:10] Estimate dispersion: DONE dispersion | min: 0.903564453125 | max: 4.679443359375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 4 cells batches from [1:4] to [13:16] Executing 1 cells batches from [17:20] to [17:20] Estimate nu: DONE nu change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014 Nu mean: 1.68489292689732 Marginal errors | max: 0.25535328937316 | median 0.0807577993228135 | mean: 0.101980750205762 Estimate dispersion: START Effective number of cores used: 1 Executing 3 genes batches from [1:3] to [8:10] Estimate dispersion: DONE dispersion | min: 1.037109375 | max: 4.6107177734375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 4 cells batches from [1:4] to [13:16] Executing 1 cells batches from [17:20] to [17:20] Estimate nu: DONE nu change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011 Nu mean: 1.69735147626627 Marginal errors | max: 0.00326864580272002 | median 0.00111524657842743 | mean: 0.00131556083122533 Estimate dispersion: START Effective number of cores used: 1 Executing 3 genes batches from [1:3] to [8:10] Estimate dispersion: DONE dispersion | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10 Estimate nu: START Effective number of cores used: 1 Executing 4 cells batches from [1:4] to [13:16] Executing 1 cells batches from [17:20] to [17:20] Estimate nu: DONE nu change (abs) | max: 0 | median: 0 | mean: 0 Nu mean: 1.69735147626627 Marginal errors | max: 7.56328383637594e-05 | median 1.72948087246994e-05 | mean: 2.99252342145451e-05 Estimate dispersion/nu: DONE Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.51865577697754 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000587224960327148 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00156569480895996 Estimating genes' coex Calculate genes' coex elapsed time: 0.726588487625122 Total calculations elapsed time: 3.24739718437195 Calculate genes' coex (legacy): DONE Calculating S: START Calculating S: DONE Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Calculating G: DONE Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values genome wide on columns and genome wide on rows calculating PValues: DONE Using G Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Calculating G: DONE calculating PValues: START Get p-values on a set of genes on columns and on a set of genes on rows calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE Calculate GDI dataframe: START Using G Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Calculating G: DONE S matrix sorted Calculate GDI dataframe: DONE Calculating S: START Calculating S: DONE S matrix sorted S matrix sorted Initializing `COTAN` meta-data Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 3.04552388191223 Cotan genes' coex estimation started Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.84900069236755 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00576329231262207 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.046055793762207 Estimating genes' coex Calculate genes' coex elapsed time: 0.794932126998901 Total calculations elapsed time: 3.69575190544128 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.39322471618652 Total elapsed time: 8.17165780067444 Initializing `COTAN` meta-data Condition test n cells 1200 Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 3.10868239402771 Cotan genes' coex estimation started Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.0062689781189 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00672507286071777 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0471436977386475 Estimating genes' coex Calculate genes' coex elapsed time: 0.782883167266846 Total calculations elapsed time: 3.84302091598511 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.61403155326843 Total elapsed time: 8.57299566268921 Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Condition test n cells 1200 Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 3.06238913536072 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.66256523132324 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00639104843139648 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0491869449615479 Estimating genes' coex Calculate genes' coex elapsed time: 0.925704717636108 Total calculations elapsed time: 3.64384794235229 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.39762115478516 Total elapsed time: 8.29691886901855 Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Condition test n cells 1200 Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 3.34205102920532 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.76953196525574 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00540518760681152 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0450568199157715 Estimating genes' coex Calculate genes' coex elapsed time: 0.776563167572021 Total calculations elapsed time: 3.59655714035034 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.44161128997803 Total elapsed time: 8.61751818656921 Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Asked to drop 0 genes and 1160 cells Cotan analysis functions started Asked to drop 31 genes and 0 cells Genes/cells selection done: dropped [31] genes and [0] cells Working on [569] genes and [40] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:569] to [1:569] Estimate dispersion: DONE dispersion | min: -0.2119140625 | max: 85.5 | % negative: 62.2144112478032 Cotan genes' coex estimation not requested Total elapsed time: 4.16460204124451 Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.62762641906738 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00617885589599609 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00644683837890625 Estimating genes' coex Calculate genes' coex elapsed time: 0.96510648727417 Total calculations elapsed time: 3.60535860061646 Calculate genes' coex (legacy): DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.72195363044739 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00560426712036133 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00638961791992188 Estimating genes' coex Calculate genes' coex elapsed time: 0.812095165252686 Total calculations elapsed time: 3.54604268074036 Calculate genes' coex (legacy): DONE While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.32270240783691 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00573372840881348 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00633645057678223 Estimating genes' coex Calculate genes' coex elapsed time: 0.76508355140686 Total calculations elapsed time: 3.09985613822937 Calculate genes' coex (legacy): DONE Hangling COTAN object with condition: test Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and on a set of genes on rows calculating PValues: DONE Handling genes type: G2 Handling genes type: G3 Initializing `COTAN` meta-data Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells PCA: START PCA: DONE Hierarchical clustering: START Hierarchical clustering: DONE Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Cotan genes' coex estimation not requested Total elapsed time: 8.12284374237061 Saving elaborated data locally at: /tmp/RtmphK1egP/test.cotan.RDS Creating cells' uniform clustering: START In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters Creating Seurat object: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================================================================| 100% PC_ 1 Positive: g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528 g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583 g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541 Negative: g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140 g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135 g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128 PC_ 2 Positive: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087 g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207 g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158 Negative: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539 g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538 g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570 PC_ 3 Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360 g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470 g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317 Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303 g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262 g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241 PC_ 4 Positive: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 Negative: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 PC_ 5 Positive: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237 g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505 g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393 Negative: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578 g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381 g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272 Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1200 Number of edges: 55489 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5973 Number of communities: 4 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 0.8 22:01:58 UMAP embedding parameters a = 0.9922 b = 1.112 22:01:58 Read 1200 rows and found 50 numeric columns 22:01:58 Using Annoy for neighbor search, n_neighbors = 30 22:01:58 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 22:01:58 Writing NN index file to temp file /tmp/RtmphK1egP/file25e813293a1033 22:01:58 Searching Annoy index using 1 thread, search_k = 3000 22:01:58 Annoy recall = 100% 22:01:59 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 22:02:01 Initializing from normalized Laplacian + noise (using RSpectra) 22:02:01 Commencing optimization for 500 epochs, with 42274 positive edges Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 22:02:03 Optimization finished Creating Seurat object: DONE * checking uniformity of cluster '0' of 4 clusters Asked to drop 0 genes and 847 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [353] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.038818359375 | max: 11.109375 | % negative: 5 Only analysis elapsed time: 2.80298042297363 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.67980241775513 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00809383392333984 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0382926464080811 Estimating genes' coex Calculate genes' coex elapsed time: 0.866415023803711 Total calculations elapsed time: 3.59260392189026 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.41064262390137 Total elapsed time: 7.96947193145752 Checking uniformity for the cluster '01_0000' with 353 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0000, with size 353, is uniform 0.83% of the genes is above the given GDI threshold 1.46 highest 1% GDI quantile is at 1.4439 cluster 01_0000 is uniform * checking uniformity of cluster '1' of 4 clusters Asked to drop 0 genes and 879 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [321] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5 Only analysis elapsed time: 2.59929871559143 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.37896108627319 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0061190128326416 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0315346717834473 Estimating genes' coex Calculate genes' coex elapsed time: 0.841798543930054 Total calculations elapsed time: 3.25841331481934 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.04916477203369 Total elapsed time: 7.41541218757629 Checking uniformity for the cluster '01_0001' with 321 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0001, with size 321, is uniform 0.5% of the genes is above the given GDI threshold 1.46 highest 1% GDI quantile is at 1.4305 cluster 01_0001 is uniform * checking uniformity of cluster '2' of 4 clusters Asked to drop 0 genes and 905 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [295] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.054443359375 | max: 104 | % negative: 36.5 Only analysis elapsed time: 2.54364085197449 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.36805772781372 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00598835945129395 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0145478248596191 Estimating genes' coex Calculate genes' coex elapsed time: 0.732106447219849 Total calculations elapsed time: 3.12070035934448 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 3.90873241424561 Total elapsed time: 7.31243872642517 Checking uniformity for the cluster '01_0002' with 295 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0002, with size 295, is uniform 0% of the genes is above the given GDI threshold 1.46 highest 1% GDI quantile is at 1.3925 cluster 01_0002 is uniform * checking uniformity of cluster '3' of 4 clusters Asked to drop 0 genes and 969 cells Cotan analysis functions started Asked to drop 1 genes and 0 cells Genes/cells selection done: dropped [1] genes and [0] cells Working on [599] genes and [231] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:599] to [1:599] Estimate dispersion: DONE dispersion | min: -0.0662841796875 | max: 82.5 | % negative: 33.889816360601 Only analysis elapsed time: 2.35808825492859 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.42995810508728 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00721931457519531 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.017031192779541 Estimating genes' coex Calculate genes' coex elapsed time: 0.844678401947021 Total calculations elapsed time: 3.29888701438904 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.05604028701782 Total elapsed time: 7.20892310142517 Checking uniformity for the cluster '01_0003' with 231 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0003, with size 231, is uniform 0% of the genes is above the given GDI threshold 1.46 highest 1% GDI quantile is at 1.373 cluster 01_0003 is uniform Found 4 uniform and 0 non-uniform clusters NO new possible uniform clusters! Unclustered cell left: 0 The final raw clusterization contains [ 4 ] different clusters: 01_0000, 01_0001, 01_0002, 01_0003 Differential Expression Analysis - START * DEA on cluster '1' with 353 cells * DEA on cluster '2' with 321 cells * DEA on cluster '3' with 295 cells * DEA on cluster '4' with 231 cells Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 3, 2 -> 1, 3 -> 2, 4 -> 4 Creating cells' uniform clustering: DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4 Asked to drop 0 genes and 905 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [295] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.054443359375 | max: 104 | % negative: 36.5 Only analysis elapsed time: 2.7196888923645 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.52901887893677 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00583529472351074 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0144710540771484 Estimating genes' coex Calculate genes' coex elapsed time: 0.855519771575928 Total calculations elapsed time: 3.40484499931335 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.25292253494263 Total elapsed time: 7.8149721622467 Checking uniformity for the cluster 'Cluster_2' with 295 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster Cluster_2, with size 295, is uniform 0% of the genes is above the given GDI threshold 1.46 highest 1% GDI quantile is at 1.3925 Differential Expression Analysis - START * DEA on cluster '-1' with 50 cells * DEA on cluster '1' with 321 cells * DEA on cluster '2' with 245 cells * DEA on cluster '3' with 353 cells * DEA on cluster '4' with 231 cells Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 2, 2 -> 1, 3 -> 4, 4 -> 3, -1 -> -1 Applied reordering to clusterization is: 1 -> 2, 2 -> 3, 3 -> 1, 4 -> 4, -1 -> -1 Creating cells' uniform clustering: START In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters Creating Seurat object: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================================================================| 100% PC_ 1 Positive: g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528 g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583 g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541 Negative: g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140 g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135 g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128 PC_ 2 Positive: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087 g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207 g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158 Negative: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539 g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538 g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570 PC_ 3 Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360 g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470 g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317 Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303 g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262 g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241 PC_ 4 Positive: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 Negative: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 PC_ 5 Positive: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237 g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505 g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393 Negative: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578 g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381 g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272 Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1200 Number of edges: 55489 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5973 Number of communities: 4 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 0.8 22:03:14 UMAP embedding parameters a = 0.9922 b = 1.112 22:03:14 Read 1200 rows and found 50 numeric columns 22:03:14 Using Annoy for neighbor search, n_neighbors = 30 22:03:14 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 22:03:14 Writing NN index file to temp file /tmp/RtmphK1egP/file25e8132b97c3b1 22:03:14 Searching Annoy index using 1 thread, search_k = 3000 22:03:15 Annoy recall = 100% 22:03:16 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 22:03:17 Initializing from normalized Laplacian + noise (using RSpectra) 22:03:17 Commencing optimization for 500 epochs, with 42274 positive edges Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 22:03:20 Optimization finished Creating Seurat object: DONE Using passed in clusterization * checking uniformity of cluster '1' of 2 clusters Asked to drop 0 genes and 600 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [600] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.0386962890625 | max: 19.40625 | % negative: 6.5 Only analysis elapsed time: 2.40703535079956 Cotan genes' coex estimation started Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.52967691421509 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00556445121765137 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0341000556945801 Estimating genes' coex Calculate genes' coex elapsed time: 0.783667802810669 Total calculations elapsed time: 3.35300922393799 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.14722275733948 Total elapsed time: 7.32180762290955 Checking uniformity for the cluster '01_0001' with 600 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0001, with size 600, is uniform 1% of the genes is above the given GDI threshold 1.46 highest 1% GDI quantile is at 1.4534 cluster 01_0001 is uniform * checking uniformity of cluster '2' of 2 clusters Asked to drop 0 genes and 600 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [600] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.032958984375 | max: 10.0859375 | % negative: 3.66666666666667 Only analysis elapsed time: 2.86830997467041 Cotan genes' coex estimation started Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.65552520751953 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0055086612701416 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0368201732635498 Estimating genes' coex Calculate genes' coex elapsed time: 0.773010969161987 Total calculations elapsed time: 3.47086501121521 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.25933361053467 Total elapsed time: 7.90339851379395 Checking uniformity for the cluster '01_0002' with 600 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 01_0002, with size 600, is uniform 0.5% of the genes is above the given GDI threshold 1.46 highest 1% GDI quantile is at 1.4378 cluster 01_0002 is uniform Found 2 uniform and 0 non-uniform clusters NO new possible uniform clusters! Unclustered cell left: 0 The final raw clusterization contains [ 2 ] different clusters: 01_0001, 01_0002 Differential Expression Analysis - START * DEA on cluster '1' with 600 cells * DEA on cluster '2' with 600 cells Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Creating cells' uniform clustering: DONE findClustersMarkers - START clustersDeltaExpression - START Handling cluster '1' with mean UDE 1.20998115359079 Handling cluster '2' with mean UDE 0.538244816501366 Handling cluster '3' with mean UDE 1.43530796540674 Handling cluster '4' with mean UDE 0.632684489354434 clustersDeltaExpression - DONE Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Log Fold Change Analysis - DONE findClustersMarkers - DONE findClustersMarkers - START clustersDeltaExpression - START Handling cluster '1' with mean UDE 1.20998115359079 Handling cluster '2' with mean UDE 0.538244816501366 Handling cluster '3' with mean UDE 1.43530796540674 Handling cluster '4' with mean UDE 0.632684489354434 clustersDeltaExpression - DONE Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Log Fold Change Analysis - DONE findClustersMarkers - DONE findClustersMarkers - START Differential Expression Analysis - START * DEA on cluster '1' with 321 cells * DEA on cluster '2' with 295 cells * DEA on cluster '3' with 353 cells * DEA on cluster '4' with 231 cells Differential Expression Analysis - DONE clustersDeltaExpression - START Handling cluster '1' with mean UDE 1.20998115359079 Handling cluster '2' with mean UDE 0.538244816501366 Handling cluster '3' with mean UDE 1.43530796540674 Handling cluster '4' with mean UDE 0.632684489354434 clustersDeltaExpression - DONE Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Log Fold Change Analysis - DONE findClustersMarkers - DONE [1] "1" Asked to drop 0 genes and 879 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [321] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5 Only analysis elapsed time: 2.35528874397278 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.29314088821411 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00773930549621582 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0344362258911133 Estimating genes' coex Calculate genes' coex elapsed time: 0.721118450164795 Total calculations elapsed time: 3.05643486976624 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 3.84887480735779 Total elapsed time: 6.97525525093079 Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE [1] "3" Asked to drop 0 genes and 847 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [353] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.038818359375 | max: 11.109375 | % negative: 5 Only analysis elapsed time: 2.49554228782654 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.30667424201965 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00716781616210938 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0378773212432861 Estimating genes' coex Calculate genes' coex elapsed time: 0.764651298522949 Total calculations elapsed time: 3.116370677948 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 3.82602906227112 Total elapsed time: 7.09700512886047 Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 2.8918149471283 Cotan genes' coex estimation started Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.63839936256409 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00560355186462402 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0466868877410889 Estimating genes' coex Calculate genes' coex elapsed time: 0.796840190887451 Total calculations elapsed time: 3.48752999305725 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.33141875267029 Total elapsed time: 7.97286987304688 Calculating gene co-expression space - START Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows calculating PValues: DONE Number of selected secondary markers: 109 Calculating S: START Calculating S: DONE S matrix sorted Number of columns (V set - secondary markers): 109 Number of rows (U set): 60 Calculating gene co-expression space - DONE Establishing gene clusters - START Calculating gene co-expression space - START Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows calculating PValues: DONE Number of selected secondary markers: 109 Calculating S: START Calculating S: DONE S matrix sorted Number of columns (V set - secondary markers): 109 Number of rows (U set): 60 Calculating gene co-expression space - DONE Establishing gene clusters - DONE Initializing `COTAN` meta-data Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Cotan genes' coex estimation not requested Total elapsed time: 4.74308228492737 Differential Expression Analysis - START * DEA on cluster '1' with 353 cells * DEA on cluster '2' with 221 cells * DEA on cluster '3' with 315 cells * DEA on cluster '4' with 311 cells Differential Expression Analysis - DONE Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Log Fold Change Analysis - DONE clustersDeltaExpression - START Handling cluster '1' with mean UDE 1.43530796540674 Handling cluster '2' with mean UDE 0.640931107489519 Handling cluster '3' with mean UDE 0.546546914955575 Handling cluster '4' with mean UDE 1.22034802329657 clustersDeltaExpression - DONE In group G1 there are 3 detected over 3 genes In group G2 there are 2 detected over 2 genes In group G3 there are 5 detected over 5 genes Merging cells' uniform clustering: START Start merging nearest clusters: threshold 1.37 Start merging nearest clusters: iteration 1 Differential Expression Analysis - START * DEA on cluster '1' with 353 cells * DEA on cluster '2' with 221 cells * DEA on cluster '3' with 315 cells * DEA on cluster '4' with 311 cells Differential Expression Analysis - DONE New clusters pairs to be tested for merging: c("1", "2") c("3", "4") *1_2-merge Asked to drop 0 genes and 626 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [574] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333 Only analysis elapsed time: 2.57235717773438 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.89119029045105 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00731396675109863 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0397636890411377 Estimating genes' coex Calculate genes' coex elapsed time: 0.744971513748169 Total calculations elapsed time: 3.68323945999146 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.42199683189392 Total elapsed time: 7.75513505935669 Checking uniformity for the cluster '1_2-merge' with 574 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_2-merge, with size 574, is not uniform 6.83% of the genes is above the given GDI threshold 1.37 highest 1% GDI quantile is at 1.4297 Clusters 1 and 2 cannot be merged *3_4-merge Asked to drop 0 genes and 574 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [626] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667 Only analysis elapsed time: 2.78623986244202 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.65650367736816 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00571846961975098 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.035301685333252 Estimating genes' coex Calculate genes' coex elapsed time: 0.985988616943359 Total calculations elapsed time: 3.68351244926453 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.57489418983459 Total elapsed time: 8.12912487983704 Checking uniformity for the cluster '3_4-merge' with 626 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 3_4-merge, with size 626, is not uniform 7.17% of the genes is above the given GDI threshold 1.37 highest 1% GDI quantile is at 1.4544 Clusters 3 and 4 cannot be merged Finished the first batch - no merges were executed Start merging nearest clusters: iteration 2 Differential Expression Analysis - START * DEA on cluster '1' with 353 cells * DEA on cluster '2' with 221 cells * DEA on cluster '3' with 315 cells * DEA on cluster '4' with 311 cells Differential Expression Analysis - DONE New clusters pairs to be tested for merging: c("2", "3") c("2", "4") *2_3-merge Asked to drop 0 genes and 664 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [536] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.0390625 | max: 12.59375 | % negative: 9.16666666666667 Only analysis elapsed time: 2.706458568573 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.48645257949829 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0056002140045166 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0251152515411377 Estimating genes' coex Calculate genes' coex elapsed time: 0.723527193069458 Total calculations elapsed time: 3.2406952381134 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 3.99657511711121 Total elapsed time: 7.54317593574524 Checking uniformity for the cluster '2_3-merge' with 536 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 2_3-merge, with size 536, is not uniform 10.17% of the genes is above the given GDI threshold 1.37 highest 1% GDI quantile is at 1.4902 Clusters 2 and 3 cannot be merged *2_4-merge Asked to drop 0 genes and 668 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [532] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.04754638671875 | max: 10.234375 | % negative: 5 Only analysis elapsed time: 2.63653063774109 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.54126715660095 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00793671607971191 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.037555456161499 Estimating genes' coex Calculate genes' coex elapsed time: 0.812577724456787 Total calculations elapsed time: 3.39933705329895 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.2127583026886 Total elapsed time: 7.68725943565369 Checking uniformity for the cluster '2_4-merge' with 532 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 2_4-merge, with size 532, is not uniform 22.5% of the genes is above the given GDI threshold 1.37 highest 1% GDI quantile is at 1.5909 Clusters 2 and 4 cannot be merged None of the 4 tested cluster pairs could be merged Executed all merges for threshold 1.37 Start merging nearest clusters: threshold 1.4 Start merging nearest clusters: iteration 3 Differential Expression Analysis - START * DEA on cluster '1' with 353 cells * DEA on cluster '2' with 221 cells * DEA on cluster '3' with 315 cells * DEA on cluster '4' with 311 cells Differential Expression Analysis - DONE New clusters pairs to be tested for merging: c("1", "3") c("1", "4") *1_3-merge Asked to drop 0 genes and 532 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [668] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.046630859375 | max: 9.03515625 | % negative: 1.33333333333333 Only analysis elapsed time: 2.71045923233032 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.81070232391357 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00570058822631836 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0388076305389404 Estimating genes' coex Calculate genes' coex elapsed time: 0.77536678314209 Total calculations elapsed time: 3.63057732582092 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.43421745300293 Total elapsed time: 7.93564581871033 Checking uniformity for the cluster '1_3-merge' with 668 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_3-merge, with size 668, is not uniform 32.67% of the genes is above the given GDI threshold 1.4 highest 1% GDI quantile is at 1.657 Clusters 1 and 3 cannot be merged *1_4-merge Asked to drop 0 genes and 536 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [664] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.0164794921875 | max: 5.5595703125 | % negative: 0.166666666666667 Only analysis elapsed time: 2.60391116142273 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.30320191383362 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00722742080688477 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0452253818511963 Estimating genes' coex Calculate genes' coex elapsed time: 0.724405527114868 Total calculations elapsed time: 3.08006024360657 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 3.79202771186829 Total elapsed time: 7.11015152931213 Checking uniformity for the cluster '1_4-merge' with 664 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_4-merge, with size 664, is not uniform 34.17% of the genes is above the given GDI threshold 1.4 highest 1% GDI quantile is at 1.5911 Clusters 1 and 4 cannot be merged None of the 6 tested cluster pairs could be merged Executed all merges for threshold 1.4 Start merging nearest clusters: threshold 1.43 Start merging nearest clusters: iteration 4 Differential Expression Analysis - START * DEA on cluster '1' with 353 cells * DEA on cluster '2' with 221 cells * DEA on cluster '3' with 315 cells * DEA on cluster '4' with 311 cells Differential Expression Analysis - DONE New clusters pairs to be tested for merging: Clusters 1 and 2 will be merged Executed 1 merges out of potentially 6 Start merging nearest clusters: iteration 5 Differential Expression Analysis - START * DEA on cluster '1_2-merge' with 574 cells * DEA on cluster '3' with 315 cells * DEA on cluster '4' with 311 cells Differential Expression Analysis - DONE New clusters pairs to be tested for merging: c("1_2-merge", "3") c("1_2-merge", "4") *1_2-merge_3-merge Asked to drop 0 genes and 311 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [889] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.04052734375 | max: 9.234375 | % negative: 1.16666666666667 Only analysis elapsed time: 2.73760890960693 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.81115317344666 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00590062141418457 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0400652885437012 Estimating genes' coex Calculate genes' coex elapsed time: 0.916269063949585 Total calculations elapsed time: 3.77338814735413 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.62126994132996 Total elapsed time: 8.09874391555786 Checking uniformity for the cluster '1_2-merge_3-merge' with 889 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_2-merge_3-merge, with size 889, is not uniform 15.33% of the genes is above the given GDI threshold 1.43 highest 1% GDI quantile is at 1.5775 Clusters 1_2-merge and 3 cannot be merged *1_2-merge_4-merge Asked to drop 0 genes and 315 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [885] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.01153564453125 | max: 6.0224609375 | % negative: 0.166666666666667 Only analysis elapsed time: 2.80287289619446 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.77281188964844 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00610494613647461 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0457687377929688 Estimating genes' coex Calculate genes' coex elapsed time: 0.726081848144531 Total calculations elapsed time: 3.55076742172241 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.29276871681213 Total elapsed time: 7.84469795227051 Checking uniformity for the cluster '1_2-merge_4-merge' with 885 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_2-merge_4-merge, with size 885, is not uniform 22.67% of the genes is above the given GDI threshold 1.43 highest 1% GDI quantile is at 1.6496 Clusters 1_2-merge and 4 cannot be merged None of the 8 tested cluster pairs could be merged Executed all merges for threshold 1.43 Start merging nearest clusters: threshold 1.46 Start merging nearest clusters: iteration 6 Differential Expression Analysis - START * DEA on cluster '1_2-merge' with 574 cells * DEA on cluster '3' with 315 cells * DEA on cluster '4' with 311 cells Differential Expression Analysis - DONE New clusters pairs to be tested for merging: Clusters 3 and 4 will be merged Executed 1 merges out of potentially 8 Start merging nearest clusters: iteration 7 Differential Expression Analysis - START * DEA on cluster '1_2-merge' with 574 cells * DEA on cluster '3_4-merge' with 626 cells Differential Expression Analysis - DONE New clusters pairs to be tested for merging: c("1_2-merge", "3_4-merge") *1_2-merge_3_4-merge-merge Asked to drop no genes or cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 2.96951913833618 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.69396877288818 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00550532341003418 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0450356006622314 Estimating genes' coex Calculate genes' coex elapsed time: 0.778393268585205 Total calculations elapsed time: 3.52290296554565 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.32058763504028 Total elapsed time: 8.04455184936523 Checking uniformity for the cluster '1_2-merge_3_4-merge-merge' with 1200 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_2-merge_3_4-merge-merge, with size 1200, is not uniform 22.17% of the genes is above the given GDI threshold 1.46 highest 1% GDI quantile is at 1.6405 Clusters 1_2-merge and 3_4-merge cannot be merged None of the 9 tested cluster pairs could be merged Executed all merges for threshold 1.46 The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge Differential Expression Analysis - START * DEA on cluster '1' with 574 cells * DEA on cluster '2' with 626 cells Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Merging cells' uniform clustering: DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' Log Fold Change Analysis - DONE Asked to drop 0 genes and 626 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [574] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333 Only analysis elapsed time: 2.74944877624512 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.61085534095764 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00665712356567383 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0401644706726074 Estimating genes' coex Calculate genes' coex elapsed time: 0.821825742721558 Total calculations elapsed time: 3.47950267791748 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.38998341560364 Total elapsed time: 7.92247819900513 Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE Asked to drop 0 genes and 574 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [626] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667 Only analysis elapsed time: 2.84521532058716 Cotan genes' coex estimation started While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.8537974357605 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.007568359375 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0377459526062012 Estimating genes' coex Calculate genes' coex elapsed time: 0.783540010452271 Total calculations elapsed time: 3.68265175819397 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.4390983581543 Total elapsed time: 8.03443169593811 Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE [ FAIL 0 | WARN 0 | SKIP 0 | PASS 452 ] > > proc.time() user system elapsed 630.996 5.862 629.622
COTAN.Rcheck/COTAN-Ex.timings
name | user | system | elapsed | |
COTAN-Legacy | 0.003 | 0.000 | 0.003 | |
COTANObjectCreation | 8.759 | 0.256 | 8.700 | |
CalculatingCOEX | 54.522 | 1.585 | 54.708 | |
ClustersList | 0.004 | 0.003 | 0.008 | |
GenesStatistics | 10.862 | 0.201 | 10.704 | |
HandleMetaData | 0.091 | 0.004 | 0.095 | |
HandlingClusterizations | 30.237 | 0.566 | 30.705 | |
HandlingConditions | 0.094 | 0.000 | 0.094 | |
HeatmapPlots | 33.610 | 0.725 | 33.329 | |
LoggingFunctions | 0.002 | 0.000 | 0.002 | |
ParametersEstimations | 24.326 | 0.227 | 24.533 | |
RawDataCleaning | 4.354 | 0.028 | 4.297 | |
RawDataGetters | 0.071 | 0.000 | 0.071 | |
UniformClusters | 189.885 | 0.899 | 188.343 | |
getColorsVector | 0.001 | 0.000 | 0.001 | |