Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-07-04 11:44 -0400 (Thu, 04 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4411 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4413 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4395 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4390 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4407 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 436/2243 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
COTAN 2.5.6 (landing page) Galfrè Silvia Giulia
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the COTAN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COTAN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: COTAN |
Version: 2.5.6 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings COTAN_2.5.6.tar.gz |
StartedAt: 2024-07-04 03:55:27 -0000 (Thu, 04 Jul 2024) |
EndedAt: 2024-07-04 04:20:00 -0000 (Thu, 04 Jul 2024) |
EllapsedTime: 1473.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: COTAN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings COTAN_2.5.6.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/COTAN.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘COTAN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘COTAN’ version ‘2.5.6’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘COTAN’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘torch’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Unexported object imported by a ':::' call: ‘ggplot2:::ggname’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GDIPlot: no visible binding for global variable ‘sum.raw.norm’ GDIPlot: no visible binding for global variable ‘GDI’ UMAPPlot: no visible binding for global variable ‘x’ UMAPPlot: no visible binding for global variable ‘y’ UMAPPlot: no visible binding for global variable ‘types’ calculateCoex_Legacy: no visible binding for global variable ‘expectedNN’ calculateCoex_Legacy: no visible binding for global variable ‘expectedNY’ calculateCoex_Legacy: no visible binding for global variable ‘expectedYN’ calculateCoex_Legacy: no visible binding for global variable ‘expectedYY’ calculateCoex_Legacy: no visible binding for global variable ‘observedYY’ calculateCoex_Legacy: no visible binding for global variable ‘.’ calculateG: no visible binding for global variable ‘observedNN’ calculateG: no visible binding for global variable ‘observedNY’ calculateG: no visible binding for global variable ‘observedYN’ calculateG: no visible binding for global variable ‘observedYY’ calculateG: no visible binding for global variable ‘expectedNN’ calculateG: no visible binding for global variable ‘expectedNY’ calculateG: no visible binding for global variable ‘expectedYN’ calculateG: no visible binding for global variable ‘expectedYY’ calculatePartialCoex: no visible binding for global variable ‘expectedNN’ calculatePartialCoex: no visible binding for global variable ‘expectedNY’ calculatePartialCoex: no visible binding for global variable ‘expectedYN’ calculatePartialCoex: no visible binding for global variable ‘expectedYY’ calculatePartialCoex: no visible binding for global variable ‘observedYY’ calculatePartialCoex: no visible binding for global variable ‘.’ cellsUniformClustering: no visible binding for global variable ‘objSeurat’ cellsUniformClustering: no visible binding for global variable ‘usedMaxResolution’ cellsUniformClustering: no visible binding for global variable ‘permMap’ checkClusterUniformity: ... may be used in an incorrect context: ‘c(..., nuPlot, zoomedNuPlot)’ checkClusterUniformity: no visible binding for global variable ‘nuPlot’ checkClusterUniformity: no visible binding for global variable ‘zoomedNuPlot’ cleanPlots: no visible binding for global variable ‘PC1’ cleanPlots: no visible binding for global variable ‘PC2’ cleanPlots: no visible binding for global variable ‘n’ cleanPlots: no visible binding for global variable ‘means’ cleanPlots: no visible binding for global variable ‘nu’ clustersMarkersHeatmapPlot: no visible binding for global variable ‘condName’ clustersMarkersHeatmapPlot: no visible binding for global variable ‘conditions’ clustersSummaryPlot: no visible binding for global variable ‘keys’ clustersSummaryPlot: no visible binding for global variable ‘values’ clustersSummaryPlot: no visible binding for global variable ‘CellNumber’ clustersSummaryPlot: no visible binding for global variable ‘ExpGenes’ clustersSummaryPlot: no visible binding for global variable ‘Cluster’ clustersSummaryPlot: no visible binding for global variable ‘Condition’ establishGenesClusters: no visible binding for global variable ‘secondaryMarkers’ establishGenesClusters: no visible binding for global variable ‘GCS’ establishGenesClusters: no visible binding for global variable ‘rankGenes’ expectedContingencyTables: no visible binding for global variable ‘expectedN’ expectedPartialContingencyTables: no visible binding for global variable ‘expectedNN’ expectedPartialContingencyTables: no visible binding for global variable ‘expectedN’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘group’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘y’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘x’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘width’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘violinwidth’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘xmax’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘xminv’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘xmaxv’ heatmapPlot: no visible binding for global variable ‘obj’ heatmapPlot: no visible binding for global variable ‘type’ heatmapPlot: no visible binding for global variable ‘g2’ heatmapPlot: no visible binding for global variable ‘coex’ mergeUniformCellsClusters : testPairListMerge: no visible binding for global variable ‘cl1’ mergeUniformCellsClusters : testPairListMerge: no visible binding for global variable ‘cl2’ mergeUniformCellsClusters : testPairListMerge : <anonymous>: no visible binding for global variable ‘cl1’ mergeUniformCellsClusters : testPairListMerge : <anonymous>: no visible binding for global variable ‘cl2’ mergeUniformCellsClusters: no visible binding for global variable ‘permMap’ mitochondrialPercentagePlot: no visible binding for global variable ‘mit.percentage’ observedContingencyTables: no visible binding for global variable ‘observedY’ observedPartialContingencyTables: no visible binding for global variable ‘observedYY’ observedPartialContingencyTables: no visible binding for global variable ‘observedY’ scatterPlot: no visible binding for global variable ‘.x’ calculateCoex,COTAN: no visible binding for global variable ‘useTorch’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘rawNorm’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘nu’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘lambda’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘a’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘hk’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘clusters’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘clusterData’ Undefined global functions or variables: . .x CellNumber Cluster Condition ExpGenes GCS GDI PC1 PC2 a cl1 cl2 clusterData clusters coex condName conditions expectedN expectedNN expectedNY expectedYN expectedYY g2 group hk keys lambda means mit.percentage n nu nuPlot obj objSeurat observedNN observedNY observedY observedYN observedYY permMap rankGenes rawNorm secondaryMarkers sum.raw.norm type types useTorch usedMaxResolution values violinwidth width x xmax xmaxv xminv y zoomedNuPlot * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed UniformClusters 216.865 7.383 223.330 CalculatingCOEX 65.061 0.353 64.707 HeatmapPlots 43.492 1.905 44.911 HandlingClusterizations 41.403 1.163 42.636 ParametersEstimations 32.287 2.083 34.437 GenesStatistics 11.942 0.447 12.149 COTANObjectCreation 11.278 0.172 11.260 RawDataCleaning 5.447 0.087 5.478 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/COTAN.Rcheck/00check.log’ for details.
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.0/site-library’ * installing *source* package ‘COTAN’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: ... may be used in an incorrect context ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (COTAN)
COTAN.Rcheck/tests/outputTestDatasetCreation.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > # Creates the files to be reloaded by the tests for comparisons > library(zeallot) > > outputTestDatasetCreation <- function(testsDir = file.path("tests", + "testthat")) { + utils::data("test.dataset", package = "COTAN") + options(parallelly.fork.enable = TRUE) + + obj <- COTAN(raw = test.dataset) + obj <- initializeMetaDataset(obj, GEO = " ", + sequencingMethod = "artificial", + sampleCondition = "test") + + obj <- proceedToCoex(obj, cores = 6L, saveObj = FALSE) + #saveRDS(obj, file = file.path(testsDir,"temp.RDS")) + + cells.names.test <- getCells(obj)[c(1L:10L, 591L:610L, 991L:1000L)] + genes.names.test <- getGenes(obj)[c(1L:10L, 291L:310L, 591L: 600L)] + saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS")) + saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS")) + + dispersion.test <- getDispersion(obj)[genes.names.test] + saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS")) + + raw.norm.test <- getNuNormData(obj)[genes.names.test, cells.names.test] + saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS")) + + coex.test <- getGenesCoex(obj, genes = genes.names.test, zeroDiagonal = FALSE) + saveRDS(coex.test, file.path(testsDir, "coex.test.RDS")) + + lambda.test <- getLambda(obj)[genes.names.test] + saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS")) + + GDI.test <- calculateGDI(obj) + GDI.test <- GDI.test[genes.names.test, ] + saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS")) + + nu.test <- getNu(obj)[cells.names.test] + saveRDS(nu.test, file.path(testsDir, "nu.test.RDS")) + + pval.test <- calculatePValue(obj, geneSubsetCol = genes.names.test) + saveRDS(pval.test, file.path(testsDir, "pval.test.RDS")) + + GDIThreshold <- 1.46 + ratioAboveThreshold <- 0.01 + initialResolution <- 0.8 + clusters <- cellsUniformClustering(obj, GDIThreshold = GDIThreshold, + ratioAboveThreshold = ratioAboveThreshold, + initialResolution = initialResolution, + cores = 6L, saveObj = FALSE)[["clusters"]] + saveRDS(clusters, file.path(testsDir, "clusters1.RDS")) + + coexDF <- DEAOnClusters(obj, clusters = clusters) + obj <- addClusterization(obj, clName = "clusters", + clusters = clusters, coexDF = coexDF) + + saveRDS(coexDF[genes.names.test, ], + file.path(testsDir, "coex.test.cluster1.RDS")) + + pvalDF <- pValueFromDEA(coexDF, getNumCells(obj), adjustmentMethod = "none") + + saveRDS(pvalDF[genes.names.test, ], + file.path(testsDir, "pval.test.cluster1.RDS")) + + c(mergedClusters, mCoexDF) %<-% + mergeUniformCellsClusters(objCOTAN = obj, + clusters = NULL, + GDIThreshold = GDIThreshold, + cores = 6L, + distance = "cosine", + hclustMethod = "ward.D2", + saveObj = FALSE) + + saveRDS(mergedClusters[genes.names.test], + file.path(testsDir, "cluster_data_merged.RDS")) + } > > proc.time() user system elapsed 0.219 0.024 0.228
COTAN.Rcheck/tests/spelling.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > if (requireNamespace("spelling", quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.190 0.036 0.215
COTAN.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > Sys.setenv(R_TESTS = "") > library(testthat) > library(COTAN) > test_check("COTAN") Setting new log level to 4 Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10 Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.61339211463928 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0014190673828125 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00873541831970215 Estimating genes' coex Calculate genes' coex elapsed time: 0.857089519500732 Total calculations elapsed time: 3.48063611984253 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: 2.69641184806824 Calculating genes' coex normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.00102090835571289 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00414490699768066 Estimating genes' coex Calculate genes' coex elapsed time: 0.884496212005615 Total calculations elapsed time: 3.58607387542725 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: 2.67569303512573 Calculating cells' coex normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.00100302696228027 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00305604934692383 Estimating cells' coex Calculate cells' coex elapsed time: 0.902730941772461 Total calculations elapsed time: 3.5824830532074 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: 2.57603573799133 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000740766525268555 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00207161903381348 Estimating genes' coex Calculate genes' coex elapsed time: 0.835188150405884 Total calculations elapsed time: 3.4140362739563 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: 2.60304284095764 Calculating cells' coex normalization factor Calculate cells' normalization factor elapsed time: 0.00075531005859375 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00203442573547363 Estimating cells' coex Calculate cells' coex elapsed time: 0.841541767120361 Total calculations elapsed time: 3.44737434387207 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: 2.59656858444214 Calculating genes' coex normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000978708267211914 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0020301342010498 Estimating genes' coex Calculate genes' coex elapsed time: 0.857989549636841 Total calculations elapsed time: 3.45756697654724 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: 2.61097931861877 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000731468200683594 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00200986862182617 Estimating genes' coex Calculate genes' coex elapsed time: 0.8634033203125 Total calculations elapsed time: 3.47712397575378 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: 2.69337010383606 Calculating cells' coex normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.00101757049560547 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00217771530151367 Estimating cells' coex Calculate cells' coex elapsed time: 0.891139507293701 Total calculations elapsed time: 3.58770489692688 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: 2.66601204872131 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000834941864013672 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00229406356811523 Estimating genes' coex Calculate genes' coex elapsed time: 0.926164865493774 Total calculations elapsed time: 3.59530591964722 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: 4.13053488731384 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: 3.15982270240784 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0216977596282959 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.055027961730957 Estimating genes' coex Calculate genes' coex elapsed time: 0.920959234237671 Total calculations elapsed time: 4.15750765800476 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.10584950447083 Total elapsed time: 10.0908389091492 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: 3.88791394233704 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: 2.90981578826904 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0203773975372314 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0592300891876221 Estimating genes' coex Calculate genes' coex elapsed time: 0.897296190261841 Total calculations elapsed time: 3.88671946525574 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.77637338638306 Total elapsed time: 9.55018472671509 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: 3.88695740699768 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: 2.92441344261169 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0207326412200928 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0526292324066162 Estimating genes' coex Calculate genes' coex elapsed time: 0.852765798568726 Total calculations elapsed time: 3.85054111480713 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.73565316200256 Total elapsed time: 9.47389888763428 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: 3.76685643196106 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: 2.93809080123901 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0197625160217285 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0534212589263916 Estimating genes' coex Calculate genes' coex elapsed time: 0.845572948455811 Total calculations elapsed time: 3.85684752464294 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.71741080284119 Total elapsed time: 9.32192349433899 Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and genome wide on rows calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE Initializing `COTAN` meta-data Asked to drop 0 genes and 1160 cells Cotan analysis functions started Asked to drop 31 genes and 0 cells Genes/cells selection done: dropped [31] genes and [0] cells Working on [569] genes and [40] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:569] to [1:569] Estimate dispersion: DONE dispersion | min: -0.2119140625 | max: 85.5 | % negative: 62.2144112478032 Cotan genes' coex estimation not requested Total elapsed time: 4.41145157814026 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: 2.83849692344666 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0185742378234863 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0085289478302002 Estimating genes' coex Calculate genes' coex elapsed time: 0.902484178543091 Total calculations elapsed time: 3.76808428764343 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: 2.72395753860474 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.018892765045166 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00929379463195801 Estimating genes' coex Calculate genes' coex elapsed time: 0.896600484848022 Total calculations elapsed time: 3.64874458312988 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: 2.71988582611084 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0180456638336182 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00853705406188965 Estimating genes' coex Calculate genes' coex elapsed time: 0.851863861083984 Total calculations elapsed time: 3.59833240509033 Calculate genes' coex (legacy): DONE Hangling COTAN object with condition: test Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and on a set of genes on rows calculating PValues: DONE Handling genes type: G2 Handling genes type: G3 Initializing `COTAN` meta-data Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells PCA: START PCA: DONE Hierarchical clustering: START Hierarchical clustering: DONE Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Cotan genes' coex estimation not requested Total elapsed time: 9.81231188774109 Saving elaborated data locally at: /home/biocbuild/tmp/RtmpE4Ydse/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-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 Negative: 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 PC_ 2 Positive: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087 g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207 g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158 Negative: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539 g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538 g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570 PC_ 3 Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360 g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470 g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317 Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303 g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262 g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241 PC_ 4 Positive: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 Negative: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 PC_ 5 Positive: g-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 Negative: 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 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 04:13:40 UMAP embedding parameters a = 0.9922 b = 1.112 04:13:40 Read 1200 rows and found 50 numeric columns 04:13:40 Using Annoy for neighbor search, n_neighbors = 30 04:13:40 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 04:13:41 Writing NN index file to temp file /home/biocbuild/tmp/RtmpE4Ydse/file259801bd5ba43 04:13:41 Searching Annoy index using 1 thread, search_k = 3000 04:13:41 Annoy recall = 100% 04:13:42 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 04:13:44 Initializing from normalized Laplacian + noise (using RSpectra) 04:13:44 Commencing optimization for 500 epochs, with 42268 positive edges Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 04:13:47 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: 3.03818798065186 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: 2.89340043067932 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0218136310577393 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0419485569000244 Estimating genes' coex Calculate genes' coex elapsed time: 0.915267705917358 Total calculations elapsed time: 3.87243032455444 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.78227972984314 Total elapsed time: 8.73183798789978 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: 3.01668858528137 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: 2.85540246963501 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0208978652954102 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0360374450683594 Estimating genes' coex Calculate genes' coex elapsed time: 0.942679643630981 Total calculations elapsed time: 3.85501742362976 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.76741480827332 Total elapsed time: 8.67852115631104 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: 2.93836355209351 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: 2.81176590919495 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0197954177856445 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0164129734039307 Estimating genes' coex Calculate genes' coex elapsed time: 0.902849197387695 Total calculations elapsed time: 3.75082349777222 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.70716881752014 Total elapsed time: 8.58866739273071 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: 2.91767382621765 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: 2.79908418655396 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.020108699798584 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0188088417053223 Estimating genes' coex Calculate genes' coex elapsed time: 0.909046649932861 Total calculations elapsed time: 3.74704837799072 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.64467024803162 Total elapsed time: 8.49534010887146 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: 2.95945882797241 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: 2.90809488296509 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0191774368286133 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0173590183258057 Estimating genes' coex Calculate genes' coex elapsed time: 0.928073883056641 Total calculations elapsed time: 3.87270522117615 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.79949045181274 Total elapsed time: 8.69174861907959 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-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 Negative: 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 PC_ 2 Positive: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087 g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207 g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158 Negative: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539 g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538 g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570 PC_ 3 Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360 g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470 g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317 Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303 g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262 g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241 PC_ 4 Positive: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 Negative: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 PC_ 5 Positive: g-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 Negative: 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 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 04:15:07 UMAP embedding parameters a = 0.9922 b = 1.112 04:15:07 Read 1200 rows and found 50 numeric columns 04:15:07 Using Annoy for neighbor search, n_neighbors = 30 04:15:07 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 04:15:08 Writing NN index file to temp file /home/biocbuild/tmp/RtmpE4Ydse/file25980144fbb198 04:15:08 Searching Annoy index using 1 thread, search_k = 3000 04:15:08 Annoy recall = 100% 04:15:09 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 04:15:11 Initializing from normalized Laplacian + noise (using RSpectra) 04:15:11 Commencing optimization for 500 epochs, with 42268 positive edges Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 04:15:14 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: 3.24190664291382 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: 3.01313257217407 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0207123756408691 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0409643650054932 Estimating genes' coex Calculate genes' coex elapsed time: 1.02825260162354 Total calculations elapsed time: 4.10306191444397 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.08949542045593 Total elapsed time: 9.24554800987244 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: 3.43908524513245 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: 2.97491312026978 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0203902721405029 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0430276393890381 Estimating genes' coex Calculate genes' coex elapsed time: 0.982210159301758 Total calculations elapsed time: 4.02054119110107 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.98335695266724 Total elapsed time: 9.35831594467163 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: 3.05311870574951 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: 2.93928456306458 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0234541893005371 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0381941795349121 Estimating genes' coex Calculate genes' coex elapsed time: 0.934790849685669 Total calculations elapsed time: 3.93572378158569 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.84251689910889 Total elapsed time: 8.82476282119751 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: 3.11666393280029 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: 3.11154913902283 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0216641426086426 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0460515022277832 Estimating genes' coex Calculate genes' coex elapsed time: 0.994767665863037 Total calculations elapsed time: 4.17403244972229 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.1276261806488 Total elapsed time: 9.21847748756409 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: 4.16163635253906 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: 3.17044425010681 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0201752185821533 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0554723739624023 Estimating genes' coex Calculate genes' coex elapsed time: 0.911723852157593 Total calculations elapsed time: 4.15781569480896 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.08209538459778 Total elapsed time: 10.1902828216553 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: 5.89905261993408 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: 3.24037647247314 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: 2.86844778060913 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0200564861297607 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0422565937042236 Estimating genes' coex Calculate genes' coex elapsed time: 0.899155616760254 Total calculations elapsed time: 3.82991647720337 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.73226165771484 Total elapsed time: 8.87924242019653 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: 3.44619464874268 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: 2.93523669242859 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0195498466491699 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0394797325134277 Estimating genes' coex Calculate genes' coex elapsed time: 0.919846057891846 Total calculations elapsed time: 3.91411232948303 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.8442907333374 Total elapsed time: 9.22795629501343 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: 3.21421408653259 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: 2.95319938659668 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0188970565795898 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0287725925445557 Estimating genes' coex Calculate genes' coex elapsed time: 0.902279853820801 Total calculations elapsed time: 3.90314888954163 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.84976100921631 Total elapsed time: 8.97480845451355 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: 3.20435237884521 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: 2.98017930984497 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0214736461639404 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0413522720336914 Estimating genes' coex Calculate genes' coex elapsed time: 0.940344333648682 Total calculations elapsed time: 3.98334956169128 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.95847511291504 Total elapsed time: 9.10565042495728 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: 3.369704246521 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: 2.9207866191864 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0213899612426758 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0438222885131836 Estimating genes' coex Calculate genes' coex elapsed time: 0.91072940826416 Total calculations elapsed time: 3.89672827720642 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.81597423553467 Total elapsed time: 9.10534596443176 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: 3.41943168640137 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: 2.960604429245 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0210671424865723 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0507087707519531 Estimating genes' coex Calculate genes' coex elapsed time: 0.968513488769531 Total calculations elapsed time: 4.00089383125305 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 4.93735980987549 Total elapsed time: 9.28701329231262 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: 4.00038766860962 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: 3.2562460899353 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0214049816131592 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0473001003265381 Estimating genes' coex Calculate genes' coex elapsed time: 1.01404118537903 Total calculations elapsed time: 4.33899235725403 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.32410430908203 Total elapsed time: 10.275759935379 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: 3.71259760856628 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: 3.10018134117126 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.023543119430542 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0544304847717285 Estimating genes' coex Calculate genes' coex elapsed time: 0.913883209228516 Total calculations elapsed time: 4.09203815460205 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.06320977210999 Total elapsed time: 9.74423360824585 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: 4.38012552261353 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: 3.25983738899231 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0215041637420654 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0544502735137939 Estimating genes' coex Calculate genes' coex elapsed time: 0.965985298156738 Total calculations elapsed time: 4.30177712440491 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.26245164871216 Total elapsed time: 10.5626022815704 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: 3.41197443008423 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: 3.20486736297607 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0215613842010498 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0451254844665527 Estimating genes' coex Calculate genes' coex elapsed time: 0.997390747070312 Total calculations elapsed time: 4.26894497871399 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.29470109939575 Total elapsed time: 9.66372847557068 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: 3.51311707496643 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: 3.09435844421387 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0208022594451904 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0411021709442139 Estimating genes' coex Calculate genes' coex elapsed time: 0.939438819885254 Total calculations elapsed time: 4.09570169448853 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.09240245819092 Total elapsed time: 9.61090636253357 Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE [ FAIL 0 | WARN 0 | SKIP 0 | PASS 452 ] > > proc.time() user system elapsed 727.428 16.334 741.995
COTAN.Rcheck/COTAN-Ex.timings
name | user | system | elapsed | |
COTAN-Legacy | 0.003 | 0.000 | 0.003 | |
COTANObjectCreation | 11.278 | 0.172 | 11.260 | |
CalculatingCOEX | 65.061 | 0.353 | 64.707 | |
ClustersList | 0.007 | 0.004 | 0.010 | |
GenesStatistics | 11.942 | 0.447 | 12.149 | |
HandleMetaData | 0.103 | 0.008 | 0.111 | |
HandlingClusterizations | 41.403 | 1.163 | 42.636 | |
HandlingConditions | 0.143 | 0.004 | 0.147 | |
HeatmapPlots | 43.492 | 1.905 | 44.911 | |
LoggingFunctions | 0.003 | 0.000 | 0.002 | |
ParametersEstimations | 32.287 | 2.083 | 34.437 | |
RawDataCleaning | 5.447 | 0.087 | 5.478 | |
RawDataGetters | 0.112 | 0.000 | 0.113 | |
UniformClusters | 216.865 | 7.383 | 223.330 | |
getColorsVector | 0.000 | 0.001 | 0.001 | |