Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:42 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 435/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
COTAN 2.5.2 (landing page) Galfrè Silvia Giulia
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the COTAN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COTAN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: COTAN |
Version: 2.5.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_2.5.2.tar.gz |
StartedAt: 2024-06-10 15:58:27 -0400 (Mon, 10 Jun 2024) |
EndedAt: 2024-06-10 16:23:17 -0400 (Mon, 10 Jun 2024) |
EllapsedTime: 1490.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: COTAN.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:COTAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings COTAN_2.5.2.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/COTAN.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘COTAN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘COTAN’ version ‘2.5.2’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘COTAN’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘torch’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Unexported object imported by a ':::' call: ‘ggplot2:::ggname’ See the note in ?`:::` about the use of this operator. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE GDIPlot: no visible binding for global variable ‘sum.raw.norm’ GDIPlot: no visible binding for global variable ‘GDI’ UMAPPlot: no visible binding for global variable ‘x’ UMAPPlot: no visible binding for global variable ‘y’ calculateCoex_Legacy: no visible binding for global variable ‘expectedNN’ calculateCoex_Legacy: no visible binding for global variable ‘expectedNY’ calculateCoex_Legacy: no visible binding for global variable ‘expectedYN’ calculateCoex_Legacy: no visible binding for global variable ‘expectedYY’ calculateCoex_Legacy: no visible binding for global variable ‘observedYY’ calculateCoex_Legacy: no visible binding for global variable ‘.’ calculateG: no visible binding for global variable ‘observedNN’ calculateG: no visible binding for global variable ‘observedNY’ calculateG: no visible binding for global variable ‘observedYN’ calculateG: no visible binding for global variable ‘observedYY’ calculateG: no visible binding for global variable ‘expectedNN’ calculateG: no visible binding for global variable ‘expectedNY’ calculateG: no visible binding for global variable ‘expectedYN’ calculateG: no visible binding for global variable ‘expectedYY’ calculatePartialCoex: no visible binding for global variable ‘expectedNN’ calculatePartialCoex: no visible binding for global variable ‘expectedNY’ calculatePartialCoex: no visible binding for global variable ‘expectedYN’ calculatePartialCoex: no visible binding for global variable ‘expectedYY’ calculatePartialCoex: no visible binding for global variable ‘observedYY’ calculatePartialCoex: no visible binding for global variable ‘.’ cellsUniformClustering: no visible binding for global variable ‘objSeurat’ cellsUniformClustering: no visible binding for global variable ‘usedMaxResolution’ cellsUniformClustering: no visible binding for global variable ‘permMap’ checkClusterUniformity: ... may be used in an incorrect context: ‘c(..., nuPlot, zoomedNuPlot)’ checkClusterUniformity: no visible binding for global variable ‘nuPlot’ checkClusterUniformity: no visible binding for global variable ‘zoomedNuPlot’ cleanPlots: no visible binding for global variable ‘PC1’ cleanPlots: no visible binding for global variable ‘PC2’ cleanPlots: no visible binding for global variable ‘n’ cleanPlots: no visible binding for global variable ‘means’ cleanPlots: no visible binding for global variable ‘nu’ clustersMarkersHeatmapPlot: no visible binding for global variable ‘condName’ clustersMarkersHeatmapPlot: no visible binding for global variable ‘conditions’ clustersSummaryPlot: no visible binding for global variable ‘keys’ clustersSummaryPlot: no visible binding for global variable ‘values’ clustersSummaryPlot: no visible binding for global variable ‘CellNumber’ clustersSummaryPlot: no visible binding for global variable ‘ExpGenes’ clustersSummaryPlot: no visible binding for global variable ‘Cluster’ clustersSummaryPlot: no visible binding for global variable ‘Condition’ establishGenesClusters: no visible binding for global variable ‘secondaryMarkers’ establishGenesClusters: no visible binding for global variable ‘GCS’ establishGenesClusters: no visible binding for global variable ‘rankGenes’ expectedContingencyTables: no visible binding for global variable ‘expectedN’ expectedPartialContingencyTables: no visible binding for global variable ‘expectedNN’ expectedPartialContingencyTables: no visible binding for global variable ‘expectedN’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘group’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘y’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘x’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘width’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘violinwidth’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘xmax’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘xminv’ geom_flat_violin : <anonymous>: no visible binding for global variable ‘xmaxv’ heatmapPlot: no visible binding for global variable ‘g2’ mergeUniformCellsClusters : testPairListMerge: no visible binding for global variable ‘cl1’ mergeUniformCellsClusters : testPairListMerge: no visible binding for global variable ‘cl2’ mergeUniformCellsClusters: no visible binding for global variable ‘permMap’ mitochondrialPercentagePlot: no visible binding for global variable ‘mit.percentage’ observedContingencyTables: no visible binding for global variable ‘observedY’ observedPartialContingencyTables: no visible binding for global variable ‘observedYY’ observedPartialContingencyTables: no visible binding for global variable ‘observedY’ scatterPlot: no visible binding for global variable ‘.x’ calculateCoex,COTAN: no visible binding for global variable ‘useTorch’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘rawNorm’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘nu’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘lambda’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘a’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘hk’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘clusters’ coerce,COTAN-scCOTAN: no visible binding for global variable ‘clusterData’ Undefined global functions or variables: . .x CellNumber Cluster Condition ExpGenes GCS GDI PC1 PC2 a cl1 cl2 clusterData clusters condName conditions expectedN expectedNN expectedNY expectedYN expectedYY g2 group hk keys lambda means mit.percentage n nu nuPlot objSeurat observedNN observedNY observedY observedYN observedYY permMap rankGenes rawNorm secondaryMarkers sum.raw.norm 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 196.509 1.979 199.603 CalculatingCOEX 73.134 1.293 76.197 HeatmapPlots 56.990 1.778 59.382 ParametersEstimations 33.042 0.957 34.428 HandlingClusterizations 28.209 0.610 29.357 GenesStatistics 14.279 0.241 14.831 COTANObjectCreation 12.837 0.270 13.432 RawDataCleaning 8.352 0.167 8.549 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘outputTestDatasetCreation.R’ Running ‘spelling.R’ Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/COTAN.Rcheck/00check.log’ for details.
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘COTAN’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: ... may be used in an incorrect context ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (COTAN)
COTAN.Rcheck/tests/outputTestDatasetCreation.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > # Creates the files to be reloaded by the tests for comparisons > library(zeallot) > > outputTestDatasetCreation <- function(testsDir = file.path("tests", + "testthat")) { + utils::data("test.dataset", package = "COTAN") + options(parallelly.fork.enable = TRUE) + + obj <- COTAN(raw = test.dataset) + obj <- initializeMetaDataset(obj, GEO = " ", + sequencingMethod = "artificial", + sampleCondition = "test") + + obj <- proceedToCoex(obj, cores = 6L, saveObj = FALSE) + #saveRDS(obj, file = file.path(testsDir,"temp.RDS")) + + cells.names.test <- getCells(obj)[c(1L:10L, 591L:610L, 991L:1000L)] + genes.names.test <- getGenes(obj)[c(1L:10L, 291L:310L, 591L: 600L)] + saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS")) + saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS")) + + dispersion.test <- getDispersion(obj)[genes.names.test] + saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS")) + + raw.norm.test <- getNormalizedData(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 + initialResolution <- 0.8 + + clusters <- cellsUniformClustering(obj, GDIThreshold = GDIThreshold, + initialResolution = initialResolution, + cores = 6L, saveObj = FALSE)[["clusters"]] + saveRDS(clusters, file.path(testsDir, "clusters1.RDS")) + + coexDF <- DEAOnClusters(obj, clusters = clusters) + obj <- addClusterization(obj, clName = "clusters", + clusters = clusters, coexDF = coexDF) + + saveRDS(coexDF[genes.names.test, ], + file.path(testsDir, "coex.test.cluster1.RDS")) + + pvalDF <- pValueFromDEA(coexDF, getNumCells(obj), method = "none") + + saveRDS(pvalDF[genes.names.test, ], + file.path(testsDir, "pval.test.cluster1.RDS")) + + c(mergedClusters, mCoexDF) %<-% + mergeUniformCellsClusters(objCOTAN = obj, + clusters = NULL, + GDIThreshold = GDIThreshold, + cores = 6L, + distance = "cosine", + hclustMethod = "ward.D2", + saveObj = FALSE) + + saveRDS(mergedClusters[genes.names.test], + file.path(testsDir, "cluster_data_merged.RDS")) + } > > proc.time() user system elapsed 0.249 0.070 0.329
COTAN.Rcheck/tests/spelling.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > if (requireNamespace('spelling', quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.230 0.069 0.307
COTAN.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > Sys.setenv(R_TESTS = "") > library(testthat) > library(COTAN) > test_check("COTAN") Setting new log level to 4 Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:10] to [1:10] Estimate dispersion: DONE dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10 Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 2.90431094169617 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00140500068664551 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00720310211181641 Estimating genes' coex Calculate genes' coex elapsed time: 0.964839935302734 Total calculations elapsed time: 3.87775897979736 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: 3.15385293960571 Calculating genes' coex normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000853061676025391 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00369501113891602 Estimating genes' coex Calculate genes' coex elapsed time: 1.03371095657349 Total calculations elapsed time: 4.19211196899414 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: 3.18256306648254 Calculating cells' coex normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.000824928283691406 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00273394584655762 Estimating cells' coex Calculate cells' coex elapsed time: 1.04579520225525 Total calculations elapsed time: 4.23191714286804 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: 0.61937543089282 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 0.026270214227825 | 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: 3.27259397506714 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000665903091430664 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00251102447509766 Estimating genes' coex Calculate genes' coex elapsed time: 1.05907106399536 Total calculations elapsed time: 4.33484196662903 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: 3.2079119682312 Calculating cells' coex normalization factor Calculate cells' normalization factor elapsed time: 0.000668048858642578 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00163388252258301 Estimating cells' coex Calculate cells' coex elapsed time: 1.0794370174408 Total calculations elapsed time: 4.28965091705322 Calculate cells' 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: 0.325 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: 3.15078616142273 Calculating genes' coex normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000851869583129883 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00171303749084473 Estimating genes' coex Calculate genes' coex elapsed time: 1.07831597328186 Total calculations elapsed time: 4.23166704177856 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: 3.17959785461426 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00064396858215332 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00251007080078125 Estimating genes' coex Calculate genes' coex elapsed time: 1.0592029094696 Total calculations elapsed time: 4.2419548034668 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: 3.18475222587585 Calculating cells' coex normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.000836849212646484 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00160408020019531 Estimating cells' coex Calculate cells' coex elapsed time: 0.976119995117188 Total calculations elapsed time: 4.16331315040588 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: 3.26459193229675 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000664949417114258 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00162291526794434 Estimating genes' coex Calculate genes' coex elapsed time: 1.01235198974609 Total calculations elapsed time: 4.2792317867279 Calculate genes' coex (legacy): DONE Calculating S: START Calculating S: DONE Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Calculating G: DONE Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values genome wide on columns and genome wide on rows calculating PValues: DONE Using G Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Calculating G: DONE calculating PValues: START Get p-values on a set of genes on columns and on a set of genes on rows calculating PValues: DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE S matrix sorted Calculate GDI dataframe: DONE Calculate GDI dataframe: START Using G Calculating G: START calculating YY.. done calculating YN..NY..NN..t().. done calculating NN.. done calculating NY..YN..YY..t().. done Estimating G Calculating G: DONE S matrix sorted Calculate GDI dataframe: DONE Calculating S: START Calculating S: DONE S matrix sorted S matrix sorted Initializing `COTAN` meta-data Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 3.98585200309753 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: 4.70516586303711 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00979900360107422 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.069965124130249 Estimating genes' coex Calculate genes' coex elapsed time: 1.02564907073975 Total calculations elapsed time: 5.81057906150818 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.8469660282135 Total elapsed time: 11.8248739242554 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: 3.73710417747498 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: 4.72972321510315 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00858283042907715 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0681569576263428 Estimating genes' coex Calculate genes' coex elapsed time: 1.03380417823792 Total calculations elapsed time: 5.84026718139648 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.94656085968018 Total elapsed time: 11.7518119812012 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: 3.98964285850525 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: 4.72870302200317 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00929808616638184 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0817780494689941 Estimating genes' coex Calculate genes' coex elapsed time: 1.06491494178772 Total calculations elapsed time: 5.88469409942627 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.9375729560852 Total elapsed time: 11.9439148902893 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: 3.98815202713013 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: 4.64286303520203 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00849580764770508 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0726161003112793 Estimating genes' coex Calculate genes' coex elapsed time: 1.06561303138733 Total calculations elapsed time: 5.78958797454834 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.86297512054443 Total elapsed time: 11.909196138382 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: 5.31567811965942 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: 3.28314805030823 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0115089416503906 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0111169815063477 Estimating genes' coex Calculate genes' coex elapsed time: 1.01693820953369 Total calculations elapsed time: 4.32271218299866 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: 3.22975897789001 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0079658031463623 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00890612602233887 Estimating genes' coex Calculate genes' coex elapsed time: 1.06363105773926 Total calculations elapsed time: 4.31026196479797 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: 3.21116399765015 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00805783271789551 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0111820697784424 Estimating genes' coex Calculate genes' coex elapsed time: 1.0656361579895 Total calculations elapsed time: 4.29604005813599 Calculate genes' coex (legacy): DONE Initializing `COTAN` meta-data Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells PCA: START PCA: DONE Hierarchical clustering: START Hierarchical clustering: DONE Estimate dispersion: START Effective number of cores used: 1 Executing 1 genes batches from [1:600] to [1:600] Estimate dispersion: DONE dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Cotan genes' coex estimation not requested Total elapsed time: 10.728245973587 Saving elaborated data locally at: /tmp/Rtmp1jPCaU/test.cotan.RDS Creating cells' uniform clustering: START In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters Creating Seurat object: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================================================================| 100% PC_ 1 Positive: g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528 g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583 g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541 Negative: g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140 g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135 g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128 PC_ 2 Positive: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087 g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207 g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158 Negative: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539 g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538 g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570 PC_ 3 Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360 g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470 g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317 Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303 g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262 g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241 PC_ 4 Positive: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 Negative: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 PC_ 5 Positive: g-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 16:17:13 UMAP embedding parameters a = 0.9922 b = 1.112 16:17:13 Read 1200 rows and found 50 numeric columns 16:17:13 Using Annoy for neighbor search, n_neighbors = 30 16:17:13 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:17:14 Writing NN index file to temp file /tmp/Rtmp1jPCaU/file4fca5d71771d 16:17:14 Searching Annoy index using 1 thread, search_k = 3000 16:17:14 Annoy recall = 100% 16:17:15 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 16:17:17 Initializing from normalized Laplacian + noise (using RSpectra) 16:17:17 Commencing optimization for 500 epochs, with 42274 positive edges Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:17:22 Optimization finished Creating PDF UMAP in file: /tmp/Rtmp1jPCaU/test/reclustering/pdf_umap_1.pdf 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: 3.51702189445496 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: 3.71599984169006 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00896310806274414 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.054426908493042 Estimating genes' coex Calculate genes' coex elapsed time: 1.13599109649658 Total calculations elapsed time: 4.91538095474243 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.05538821220398 Total elapsed time: 10.727471113205 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 GDI 99% 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: 3.65398812294006 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: 3.68317604064941 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0155000686645508 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0567858219146729 Estimating genes' coex Calculate genes' coex elapsed time: 1.13822507858276 Total calculations elapsed time: 4.8936870098114 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.05734395980835 Total elapsed time: 10.8409149646759 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 GDI 99% 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: 3.5863049030304 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: 3.61933493614197 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0116260051727295 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0240561962127686 Estimating genes' coex Calculate genes' coex elapsed time: 1.15246295928955 Total calculations elapsed time: 4.80748009681702 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.94293808937073 Total elapsed time: 10.6458768844604 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 GDI 99% 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: 3.42594504356384 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: 3.65457606315613 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00946283340454102 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0245070457458496 Estimating genes' coex Calculate genes' coex elapsed time: 1.16737008094788 Total calculations elapsed time: 4.85591602325439 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.92023086547852 Total elapsed time: 10.5228848457336 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 GDI 99% 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' * DEA on cluster '2' * DEA on cluster '3' * DEA on cluster '4' Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 3, 2 -> 1, 3 -> 2, 4 -> 4 Cluster, UMAP and Saving the Seurat dataset 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: 0.6846 Number of communities: 4 Elapsed time: 0 seconds 16:18:39 UMAP embedding parameters a = 0.9922 b = 1.112 16:18:39 Read 1200 rows and found 25 numeric columns 16:18:39 Using Annoy for neighbor search, n_neighbors = 30 16:18:39 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:18:39 Writing NN index file to temp file /tmp/Rtmp1jPCaU/file4fca9542eb9 16:18:39 Searching Annoy index using 1 thread, search_k = 3000 16:18:39 Annoy recall = 100% 16:18:40 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 16:18:43 Initializing from normalized Laplacian + noise (using RSpectra) 16:18:43 Commencing optimization for 500 epochs, with 43428 positive edges Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:18:47 Optimization finished 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: 3.58363604545593 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: 3.58654808998108 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00910186767578125 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0227751731872559 Estimating genes' coex Calculate genes' coex elapsed time: 1.15039992332458 Total calculations elapsed time: 4.7688250541687 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.89094305038452 Total elapsed time: 10.5374701023102 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 GDI 99% quantile is at 1.3925 Differential Expression Analysis - START * DEA on cluster '-1' * DEA on cluster '1' * DEA on cluster '2' * DEA on cluster '3' * DEA on cluster '4' Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 2, 2 -> 1, 3 -> 4, 4 -> 3, -1 -> -1 Applied reordering to clusterization is: 1 -> 2, 2 -> 3, 3 -> 1, 4 -> 4, -1 -> -1 Creating cells' uniform clustering: START In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters Creating Seurat object: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer counts Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================================================================| 100% PC_ 1 Positive: g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528 g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583 g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541 Negative: g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140 g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135 g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128 PC_ 2 Positive: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087 g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207 g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158 Negative: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539 g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538 g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570 PC_ 3 Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360 g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470 g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317 Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303 g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262 g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241 PC_ 4 Positive: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 Negative: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 PC_ 5 Positive: g-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 16:19:11 UMAP embedding parameters a = 0.9922 b = 1.112 16:19:11 Read 1200 rows and found 50 numeric columns 16:19:11 Using Annoy for neighbor search, n_neighbors = 30 16:19:11 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:19:11 Writing NN index file to temp file /tmp/Rtmp1jPCaU/file4fca729db314 16:19:11 Searching Annoy index using 1 thread, search_k = 3000 16:19:11 Annoy recall = 100% 16:19:12 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 16:19:15 Initializing from normalized Laplacian + noise (using RSpectra) 16:19:15 Commencing optimization for 500 epochs, with 42274 positive edges Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:19:19 Optimization finished Creating PDF UMAP in file: /tmp/Rtmp1jPCaU/test/reclustering/pdf_umap_1.pdf 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: 3.82155799865723 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: 4.06547284126282 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00916409492492676 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0548748970031738 Estimating genes' coex Calculate genes' coex elapsed time: 1.1290111541748 Total calculations elapsed time: 5.25852298736572 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.39941000938416 Total elapsed time: 11.2883720397949 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 GDI 99% 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: 3.69130086898804 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: 4.13966417312622 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0122699737548828 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0873239040374756 Estimating genes' coex Calculate genes' coex elapsed time: 1.13191413879395 Total calculations elapsed time: 5.37117218971252 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.42444109916687 Total elapsed time: 11.2666900157928 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 GDI 99% 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' * DEA on cluster '2' Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Cluster, UMAP and Saving the Seurat dataset 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: 0.6846 Number of communities: 4 Elapsed time: 0 seconds 16:20:01 UMAP embedding parameters a = 0.9922 b = 1.112 16:20:01 Read 1200 rows and found 25 numeric columns 16:20:01 Using Annoy for neighbor search, n_neighbors = 30 16:20:01 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:20:01 Writing NN index file to temp file /tmp/Rtmp1jPCaU/file4fca74fe4041 16:20:01 Searching Annoy index using 1 thread, search_k = 3000 16:20:01 Annoy recall = 100% 16:20:02 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 16:20:05 Initializing from normalized Laplacian + noise (using RSpectra) 16:20:05 Commencing optimization for 500 epochs, with 43428 positive edges Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 16:20:09 Optimization finished Creating cells' uniform clustering: DONE findClustersMarkers - START clustersDeltaExpression - START Handling cluster '1' with mean UDE 1.20998115359079 Handling cluster '2' with mean UDE 0.538244816501365 Handling cluster '3' with mean UDE 1.43530796540673 Handling cluster '4' with mean UDE 0.632684489354433 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 0.538244816501365 Handling cluster '3' with mean UDE 1.43530796540673 Handling cluster '4' with mean UDE 0.632684489354433 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' * DEA on cluster '2' * DEA on cluster '3' * DEA on cluster '4' Differential Expression Analysis - DONE clustersDeltaExpression - START Handling cluster '1' with mean UDE 1.20998115359079 Handling cluster '2' with mean UDE 0.538244816501365 Handling cluster '3' with mean UDE 1.43530796540673 Handling cluster '4' with mean UDE 0.632684489354433 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: 3.6155788898468 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: 3.65325403213501 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00863790512084961 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.047321081161499 Estimating genes' coex Calculate genes' coex elapsed time: 1.18050193786621 Total calculations elapsed time: 4.88971495628357 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.02991700172424 Total elapsed time: 10.7320199012756 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: 3.57404208183289 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: 3.7327151298523 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0113880634307861 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0559329986572266 Estimating genes' coex Calculate genes' coex elapsed time: 1.17155480384827 Total calculations elapsed time: 4.97159099578857 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.15549302101135 Total elapsed time: 10.8916709423065 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: 4.13483095169067 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: 4.94178485870361 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00820112228393555 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0710248947143555 Estimating genes' coex Calculate genes' coex elapsed time: 1.13553810119629 Total calculations elapsed time: 6.15654897689819 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 7.31259202957153 Total elapsed time: 12.5957078933716 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: 6.3512589931488 Differential Expression Analysis - START * DEA on cluster '1' * DEA on cluster '2' * DEA on cluster '3' * DEA on cluster '4' 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 1.43530796540673 Handling cluster '2' with mean UDE 0.640931107489518 Handling cluster '3' with mean UDE 0.546546914955574 Handling cluster '4' with mean UDE 1.22034802329656 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: iteration 1 Differential Expression Analysis - START * DEA on cluster '1' * DEA on cluster '2' * DEA on cluster '3' * DEA on cluster '4' Differential Expression Analysis - DONE Clusters pairs for merging: c("1", "2") c("3", "4") c("2", "3") c("2", "4") c("1", "3") c("1", "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: 3.80878686904907 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: 4.05133509635925 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00995087623596191 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0602021217346191 Estimating genes' coex Calculate genes' coex elapsed time: 1.15265989303589 Total calculations elapsed time: 5.27414798736572 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.35971713066101 Total elapsed time: 11.3607280254364 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 uniform 0.67% of the genes is above the given GDI threshold 1.46 GDI 99% quantile is at 1.4297 Clusters 1 and 2 can 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: 3.7108199596405 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: 4.10525679588318 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0104951858520508 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0564858913421631 Estimating genes' coex Calculate genes' coex elapsed time: 1.18411493301392 Total calculations elapsed time: 5.35635280609131 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.51391291618347 Total elapsed time: 11.3851699829102 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 uniform 1% of the genes is above the given GDI threshold 1.46 GDI 99% quantile is at 1.4544 Clusters 3 and 4 can be merged *Clusters 2 or 3 is now missing due to previous merges: skip. *Clusters 2 or 4 is now missing due to previous merges: skip. *Clusters 1 or 3 is now missing due to previous merges: skip. *Clusters 1 or 4 is now missing due to previous merges: skip. Executed 2 merges out of 6 Start merging nearest clusters: iteration 2 Differential Expression Analysis - START * DEA on cluster '1_2-merge' * DEA on cluster '3_4-merge' Differential Expression Analysis - DONE Clusters pairs 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: 4.18040800094604 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: 4.84555315971375 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00942087173461914 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0710630416870117 Estimating genes' coex Calculate genes' coex elapsed time: 1.17260909080505 Total calculations elapsed time: 6.09864616394043 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 7.18008208274841 Total elapsed time: 12.4624049663544 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 GDI 99% quantile is at 1.6405 Merging clusters 1_2-merge and 3_4-merge results in a too high GDI None of the 1 nearest cluster pairs could be merged The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge Differential Expression Analysis - START * DEA on cluster '1' * DEA on cluster '2' 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: 3.77642798423767 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: 4.12153315544128 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0111348628997803 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.056955099105835 Estimating genes' coex Calculate genes' coex elapsed time: 1.15912508964539 Total calculations elapsed time: 5.34874820709229 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.47019505500793 Total elapsed time: 11.3204920291901 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: 3.67376112937927 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: 4.13500809669495 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0128498077392578 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0559890270233154 Estimating genes' coex Calculate genes' coex elapsed time: 1.15643405914307 Total calculations elapsed time: 5.36028099060059 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.48402500152588 Total elapsed time: 11.3315761089325 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 433 ] > > proc.time() user system elapsed 771.815 6.808 782.915
COTAN.Rcheck/COTAN-Ex.timings
name | user | system | elapsed | |
COTAN-Legacy | 0.003 | 0.000 | 0.004 | |
COTANObjectCreation | 12.837 | 0.270 | 13.432 | |
CalculatingCOEX | 73.134 | 1.293 | 76.197 | |
ClustersList | 0.007 | 0.002 | 0.009 | |
GenesStatistics | 14.279 | 0.241 | 14.831 | |
HandleMetaData | 0.097 | 0.011 | 0.108 | |
HandlingClusterizations | 28.209 | 0.610 | 29.357 | |
HandlingConditions | 0.118 | 0.016 | 0.137 | |
HeatmapPlots | 56.990 | 1.778 | 59.382 | |
LoggingFunctions | 0.004 | 0.001 | 0.006 | |
ParametersEstimations | 33.042 | 0.957 | 34.428 | |
RawDataCleaning | 8.352 | 0.167 | 8.549 | |
RawDataGetters | 0.084 | 0.013 | 0.098 | |
UniformClusters | 196.509 | 1.979 | 199.603 | |
getColorsVector | 0.001 | 0.000 | 0.002 | |