Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-25 11:38 -0400 (Tue, 25 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4690 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4404 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" | 4353 |
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 436/2242 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
COTAN 2.5.5 (landing page) Galfrè Silvia Giulia
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | 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 | |||||||||
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: 2.5.5 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_2.5.5.tar.gz |
StartedAt: 2024-06-24 19:33:59 -0400 (Mon, 24 Jun 2024) |
EndedAt: 2024-06-24 19:55:24 -0400 (Mon, 24 Jun 2024) |
EllapsedTime: 1284.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: COTAN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_2.5.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/COTAN.Rcheck’ * using R version 4.4.1 RC (2024-06-06 r86719) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘COTAN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘COTAN’ version ‘2.5.5’ * 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 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 ‘g2’ 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 condName conditions expectedN expectedNN expectedNY expectedYN expectedYY g2 group hk keys lambda means mit.percentage n nu nuPlot objSeurat observedNN observedNY observedY observedYN observedYY permMap rankGenes rawNorm secondaryMarkers sum.raw.norm 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 185.880 3.613 188.831 CalculatingCOEX 51.270 1.131 52.812 HeatmapPlots 36.006 0.902 37.272 HandlingClusterizations 33.176 1.491 34.363 ParametersEstimations 24.678 0.777 25.691 GenesStatistics 9.934 0.430 10.276 COTANObjectCreation 8.934 0.272 9.255 RawDataCleaning 4.638 0.374 4.736 * 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 running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/COTAN.Rcheck/00check.log’ for details.
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 RC (2024-06-06 r86719) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > # 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), method = "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 0.225 0.081 0.292
COTAN.Rcheck/tests/spelling.Rout
R version 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > if (requireNamespace("spelling", quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.194 0.072 0.266
COTAN.Rcheck/tests/testthat.Rout
R version 4.4.1 RC (2024-06-06 r86719) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > 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: 2.2511510848999 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00136184692382812 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00731897354125977 Estimating genes' coex Calculate genes' coex elapsed time: 0.720044136047363 Total calculations elapsed time: 2.97987604141235 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: 2.22785019874573 Calculating genes' coex normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.00134897232055664 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00453782081604004 Estimating genes' coex Calculate genes' coex elapsed time: 0.745792150497437 Total calculations elapsed time: 2.97952914237976 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: 2.25168013572693 Calculating cells' coex normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.00103497505187988 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00333189964294434 Estimating cells' coex Calculate cells' coex elapsed time: 0.801007986068726 Total calculations elapsed time: 3.05705499649048 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: 2.22599101066589 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000597000122070312 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00188302993774414 Estimating genes' coex Calculate genes' coex elapsed time: 0.784437894821167 Total calculations elapsed time: 3.01290893554688 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: 2.35284304618835 Calculating cells' coex normalization factor Calculate cells' normalization factor elapsed time: 0.000928878784179688 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00219607353210449 Estimating cells' coex Calculate cells' coex elapsed time: 0.853915929794312 Total calculations elapsed time: 3.20988392829895 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: 2.29517197608948 Calculating genes' coex normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.00113701820373535 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00168895721435547 Estimating genes' coex Calculate genes' coex elapsed time: 0.718107223510742 Total calculations elapsed time: 3.01610517501831 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: 2.24152612686157 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000818967819213867 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0021660327911377 Estimating genes' coex Calculate genes' coex elapsed time: 0.820482969284058 Total calculations elapsed time: 3.06499409675598 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: 2.27109599113464 Calculating cells' coex normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.00104188919067383 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.0022280216217041 Estimating cells' coex Calculate cells' coex elapsed time: 0.797376155853271 Total calculations elapsed time: 3.07174205780029 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: 2.48708081245422 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000900983810424805 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00244498252868652 Estimating genes' coex Calculate genes' coex elapsed time: 0.820907115936279 Total calculations elapsed time: 3.31133389472961 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: 3.06169295310974 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: 3.05949115753174 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00878000259399414 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0442049503326416 Estimating genes' coex Calculate genes' coex elapsed time: 0.804536104202271 Total calculations elapsed time: 3.91701221466064 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.73326802253723 Total elapsed time: 8.56472396850586 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: 3.09129214286804 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: 3.0983738899231 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00856208801269531 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.051630973815918 Estimating genes' coex Calculate genes' coex elapsed time: 0.849679946899414 Total calculations elapsed time: 4.00824689865112 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.806480884552 Total elapsed time: 8.68842101097107 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: 3.1026771068573 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: 2.98405790328979 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00958418846130371 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0425868034362793 Estimating genes' coex Calculate genes' coex elapsed time: 0.804707050323486 Total calculations elapsed time: 3.84093594551086 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.64003109931946 Total elapsed time: 8.55569314956665 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: 3.03186893463135 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: 3.12368106842041 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00670599937438965 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0430259704589844 Estimating genes' coex Calculate genes' coex elapsed time: 0.780433893203735 Total calculations elapsed time: 3.95384693145752 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.77511692047119 Total elapsed time: 8.58774399757385 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: 3.95578217506409 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: 2.42733097076416 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00587296485900879 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00587010383605957 Estimating genes' coex Calculate genes' coex elapsed time: 0.796962976455688 Total calculations elapsed time: 3.23603701591492 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: 2.42569208145142 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00652289390563965 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00736618041992188 Estimating genes' coex Calculate genes' coex elapsed time: 0.789615869522095 Total calculations elapsed time: 3.22919702529907 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: 2.38301491737366 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00751996040344238 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00754499435424805 Estimating genes' coex Calculate genes' coex elapsed time: 0.795480966567993 Total calculations elapsed time: 3.19356083869934 Calculate genes' coex (legacy): 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 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: 8.17135787010193 Saving elaborated data locally at: /tmp/Rtmp4FkN3l/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-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 Negative: 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 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 19:49:33 UMAP embedding parameters a = 0.9922 b = 1.112 19:49:33 Read 1200 rows and found 50 numeric columns 19:49:33 Using Annoy for neighbor search, n_neighbors = 30 19:49:33 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:49:34 Writing NN index file to temp file /tmp/Rtmp4FkN3l/file39fd482b81a6 19:49:34 Searching Annoy index using 1 thread, search_k = 3000 19:49:34 Annoy recall = 100% 19:49:35 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 19:49:36 Initializing from normalized Laplacian + noise (using RSpectra) 19:49:36 Commencing optimization for 500 epochs, with 42270 positive edges Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:49:39 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: 2.60922288894653 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: 2.64114999771118 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00823593139648438 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0310590267181396 Estimating genes' coex Calculate genes' coex elapsed time: 0.789559125900269 Total calculations elapsed time: 3.47000408172607 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.24179315567017 Total elapsed time: 7.6177761554718 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: 2.66194295883179 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: 2.79185914993286 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0072028636932373 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0340819358825684 Estimating genes' coex Calculate genes' coex elapsed time: 0.827805995941162 Total calculations elapsed time: 3.66094994544983 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.48566699028015 Total elapsed time: 8.02203893661499 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: 2.56513094902039 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: 2.66701292991638 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00686502456665039 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0147011280059814 Estimating genes' coex Calculate genes' coex elapsed time: 0.876692056655884 Total calculations elapsed time: 3.5652711391449 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.40847992897034 Total elapsed time: 7.80759978294373 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: 2.59239816665649 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: 2.61519312858582 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00707793235778809 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0136411190032959 Estimating genes' coex Calculate genes' coex elapsed time: 0.835777997970581 Total calculations elapsed time: 3.47169017791748 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.3084089756012 Total elapsed time: 7.73929500579834 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: 2.55224704742432 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: 2.69225597381592 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00704216957092285 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0237529277801514 Estimating genes' coex Calculate genes' coex elapsed time: 0.800441980361938 Total calculations elapsed time: 3.52349305152893 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.38506889343262 Total elapsed time: 7.77512693405151 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-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 Negative: 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 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 19:50:52 UMAP embedding parameters a = 0.9922 b = 1.112 19:50:52 Read 1200 rows and found 50 numeric columns 19:50:52 Using Annoy for neighbor search, n_neighbors = 30 19:50:52 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:50:52 Writing NN index file to temp file /tmp/Rtmp4FkN3l/file39fd658e8abd 19:50:52 Searching Annoy index using 1 thread, search_k = 3000 19:50:52 Annoy recall = 100% 19:50:53 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 19:50:55 Initializing from normalized Laplacian + noise (using RSpectra) 19:50:55 Commencing optimization for 500 epochs, with 42270 positive edges Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 19:50:58 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: 2.70991516113281 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: 2.84660911560059 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00756001472473145 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0336430072784424 Estimating genes' coex Calculate genes' coex elapsed time: 0.918118953704834 Total calculations elapsed time: 3.80593109130859 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.63597393035889 Total elapsed time: 8.13708400726318 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: 2.88847494125366 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: 2.80781078338623 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00839114189147949 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0318138599395752 Estimating genes' coex Calculate genes' coex elapsed time: 0.81830620765686 Total calculations elapsed time: 3.66632199287415 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.52105689048767 Total elapsed time: 8.24448394775391 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: 2.75093698501587 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: 2.78245091438293 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00911211967468262 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0328009128570557 Estimating genes' coex Calculate genes' coex elapsed time: 0.811913013458252 Total calculations elapsed time: 3.63627696037292 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.47459411621094 Total elapsed time: 8.07507491111755 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: 2.76830816268921 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: 2.81174993515015 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00742220878601074 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0328319072723389 Estimating genes' coex Calculate genes' coex elapsed time: 0.857628107070923 Total calculations elapsed time: 3.70963215827942 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.52266192436218 Total elapsed time: 8.22238993644714 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: 3.06611800193787 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: 3.09258103370667 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00620198249816895 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0512299537658691 Estimating genes' coex Calculate genes' coex elapsed time: 0.829351186752319 Total calculations elapsed time: 3.97936415672302 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.74661087989807 Total elapsed time: 8.60282182693481 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: 4.93306088447571 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: 2.89186501502991 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: 2.77658915519714 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0102219581604004 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0374670028686523 Estimating genes' coex Calculate genes' coex elapsed time: 0.860549926757812 Total calculations elapsed time: 3.68482804298401 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.61147212982178 Total elapsed time: 8.34948420524597 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: 2.80631494522095 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: 2.80408000946045 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00653696060180664 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0381591320037842 Estimating genes' coex Calculate genes' coex elapsed time: 0.806571006774902 Total calculations elapsed time: 3.65534710884094 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.51614999771118 Total elapsed time: 8.18577408790588 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: 2.80111980438232 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: 2.8466329574585 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00580120086669922 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0281338691711426 Estimating genes' coex Calculate genes' coex elapsed time: 1.58792400360107 Total calculations elapsed time: 4.46849203109741 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.18714618682861 Total elapsed time: 9.78324413299561 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: 2.68886709213257 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: 2.7695369720459 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00582695007324219 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0325601100921631 Estimating genes' coex Calculate genes' coex elapsed time: 0.914021015167236 Total calculations elapsed time: 3.72194504737854 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.5626208782196 Total elapsed time: 8.11289286613464 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: 4.48673796653748 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: 2.78382205963135 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00705885887145996 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0372960567474365 Estimating genes' coex Calculate genes' coex elapsed time: 0.779716968536377 Total calculations elapsed time: 3.60789394378662 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.44217896461487 Total elapsed time: 10.5742688179016 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: 2.86102986335754 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: 2.82804799079895 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00808000564575195 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.045543909072876 Estimating genes' coex Calculate genes' coex elapsed time: 0.825403928756714 Total calculations elapsed time: 3.70707583427429 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.57081413269043 Total elapsed time: 8.27220511436462 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: 2.98367595672607 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: 2.83827090263367 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00539398193359375 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0350661277770996 Estimating genes' coex Calculate genes' coex elapsed time: 0.778964042663574 Total calculations elapsed time: 3.65769505500793 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.46472907066345 Total elapsed time: 8.32126402854919 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: 2.90305113792419 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: 2.99011206626892 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00790596008300781 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0450279712677002 Estimating genes' coex Calculate genes' coex elapsed time: 0.868386030197144 Total calculations elapsed time: 3.91143202781677 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.78291082382202 Total elapsed time: 8.47343182563782 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: 3.19633316993713 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: 3.15894103050232 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00679802894592285 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0425188541412354 Estimating genes' coex Calculate genes' coex elapsed time: 0.879314184188843 Total calculations elapsed time: 4.08757209777832 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.88165783882141 Total elapsed time: 8.93126082420349 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: 2.86514782905579 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: 2.82660913467407 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00585484504699707 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0357761383056641 Estimating genes' coex Calculate genes' coex elapsed time: 0.84109902381897 Total calculations elapsed time: 3.7093391418457 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.59407997131348 Total elapsed time: 8.28525900840759 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: 2.79682302474976 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: 2.86024594306946 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00677394866943359 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0327920913696289 Estimating genes' coex Calculate genes' coex elapsed time: 0.809959888458252 Total calculations elapsed time: 3.70977187156677 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.54684901237488 Total elapsed time: 8.17383623123169 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 443 ] > > proc.time() user system elapsed 645.331 10.387 661.761
COTAN.Rcheck/COTAN-Ex.timings
name | user | system | elapsed | |
COTAN-Legacy | 0.003 | 0.001 | 0.003 | |
COTANObjectCreation | 8.934 | 0.272 | 9.255 | |
CalculatingCOEX | 51.270 | 1.131 | 52.812 | |
ClustersList | 0.008 | 0.002 | 0.010 | |
GenesStatistics | 9.934 | 0.430 | 10.276 | |
HandleMetaData | 0.106 | 0.005 | 0.113 | |
HandlingClusterizations | 33.176 | 1.491 | 34.363 | |
HandlingConditions | 0.137 | 0.006 | 0.143 | |
HeatmapPlots | 36.006 | 0.902 | 37.272 | |
LoggingFunctions | 0.003 | 0.001 | 0.004 | |
ParametersEstimations | 24.678 | 0.777 | 25.691 | |
RawDataCleaning | 4.638 | 0.374 | 4.736 | |
RawDataGetters | 0.090 | 0.006 | 0.097 | |
UniformClusters | 185.880 | 3.613 | 188.831 | |
getColorsVector | 0.001 | 0.015 | 0.001 | |