Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
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 452/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
COTAN 2.8.5 (landing page) Galfrè Silvia Giulia
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the COTAN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COTAN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: COTAN |
Version: 2.8.5 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings COTAN_2.8.5.tar.gz |
StartedAt: 2025-10-14 07:52:53 -0000 (Tue, 14 Oct 2025) |
EndedAt: 2025-10-14 08:24:04 -0000 (Tue, 14 Oct 2025) |
EllapsedTime: 1871.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: COTAN.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings COTAN_2.8.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/COTAN.Rcheck’ * using R Under development (unstable) (2025-02-19 r87757) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘COTAN/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘COTAN’ version ‘2.8.5’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 27 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘COTAN’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... WARNING 'library' or 'require' call to ‘torch’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Missing or unexported object: ‘zeallot::zeallous’ * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE ECDPlot: no visible binding for global variable ‘.’ 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 ‘.’ cellSizePlot: no visible binding for global variable ‘.’ cellsUniformClustering: no visible binding for global variable ‘pca’ cellsUniformClustering: no visible binding for global variable ‘resolution’ cellsUniformClustering: no visible binding for global variable ‘usedMaxResolution’ cellsUniformClustering: no visible binding for global variable ‘permMap’ checkClusterUniformity: no visible binding for global variable ‘pcaCellsPlot’ checkClusterUniformity: no visible binding for global variable ‘.’ checkClusterUniformity: no visible binding for global variable ‘bGroupGenesPlot’ checkClusterUniformity: no visible binding for global variable ‘UDEPLot’ checkClusterUniformity: no visible binding for global variable ‘nuPlot’ checkClusterUniformity: no visible binding for global variable ‘zoomedNuPlot’ clustersMarkersHeatmapPlot: no visible binding for global variable ‘condName’ clustersMarkersHeatmapPlot: no visible binding for global variable ‘conditions’ 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’ genesSizePlot: no visible binding for global variable ‘.’ mergeUniformCellsClusters : fromMergedName: no visible binding for global variable ‘clName1’ mergeUniformCellsClusters : fromMergedName: no visible binding for global variable ‘clName2’ mergeUniformCellsClusters : testPairListMerge: no visible binding for global variable ‘cl1’ mergeUniformCellsClusters : testPairListMerge: no visible binding for global variable ‘cl2’ mergeUniformCellsClusters : mergeAllClusters : <anonymous>: no visible binding for global variable ‘clName1’ mergeUniformCellsClusters : mergeAllClusters : <anonymous>: no visible binding for global variable ‘clName2’ mergeUniformCellsClusters : mergeAllClusters: no visible binding for global variable ‘clName1’ mergeUniformCellsClusters : mergeAllClusters: no visible binding for global variable ‘clName2’ mergeUniformCellsClusters: no visible binding for global variable ‘permMap’ mitochondrialPercentagePlot: no visible binding for global variable ‘.’ 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 ‘.’ 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: . GCS UDEPLot a bGroupGenesPlot cl1 cl2 clName1 clName2 clusterData clusters condName conditions expectedN expectedNN expectedNY expectedYN expectedYY hk lambda nu nuPlot observedNN observedNY observedY observedYN observedYY pca pcaCellsPlot permMap rankGenes rawNorm resolution secondaryMarkers useTorch usedMaxResolution 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 250.703 0.709 249.103 CalculatingCOEX 73.777 0.236 71.592 HandlingClusterizations 58.176 0.159 57.848 HeatmapPlots 47.845 0.283 46.482 ParametersEstimations 34.354 0.208 34.632 GenesStatistics 15.261 0.043 14.827 COTAN_ObjectCreation 13.787 1.475 14.744 Conversions 7.854 0.028 7.897 RawDataCleaning 7.181 0.015 7.219 * 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: 1 WARNING, 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/COTAN.Rcheck/00check.log’ for details.
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘COTAN’ ... ** this is package ‘COTAN’ version ‘2.8.5’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (COTAN)
COTAN.Rcheck/tests/outputTestDatasetCreation.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > > # Creates the files to be reloaded by the tests for comparisons > library(zeallot) > > outputTestDatasetCreation <- function(testsDir = file.path("tests", + "testthat")) { + utils::data("test.dataset", package = "COTAN") + options(parallelly.fork.enable = TRUE) + + obj <- COTAN(raw = test.dataset) + obj <- initializeMetaDataset(obj, GEO = " ", + sequencingMethod = "artificial", + sampleCondition = "test") + + obj <- proceedToCoex(obj, cores = 6L, saveObj = FALSE) + #saveRDS(obj, file = file.path(testsDir,"temp.RDS")) + + cells.names.test <- getCells(obj)[c(1L:10L, 591L:610L, 991L:1000L)] + genes.names.test <- getGenes(obj)[c(1L:10L, 291L:310L, 591L: 600L)] + saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS")) + saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS")) + + dispersion.test <- getDispersion(obj)[genes.names.test] + saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS")) + + raw.norm.test <- getNuNormData(obj)[genes.names.test, cells.names.test] + saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS")) + + coex.test <- getGenesCoex(obj, genes = genes.names.test, zeroDiagonal = FALSE) + saveRDS(coex.test, file.path(testsDir, "coex.test.RDS")) + + lambda.test <- getLambda(obj)[genes.names.test] + saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS")) + + GDI.test <- calculateGDI(obj) + GDI.test <- GDI.test[genes.names.test, ] + saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS")) + + nu.test <- getNu(obj)[cells.names.test] + saveRDS(nu.test, file.path(testsDir, "nu.test.RDS")) + + pval.test <- calculatePValue(obj, geneSubsetCol = genes.names.test) + saveRDS(pval.test, file.path(testsDir, "pval.test.RDS")) + + GDIThreshold <- 1.46 + 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), adjustmentMethod = "none") + + saveRDS(pvalDF[genes.names.test, ], + file.path(testsDir, "pval.test.cluster1.RDS")) + + c(mergedClusters, mCoexDF) %<-% + mergeUniformCellsClusters(objCOTAN = obj, + clusters = NULL, + GDIThreshold = GDIThreshold, + cores = 6L, + distance = "cosine", + hclustMethod = "ward.D2", + saveObj = FALSE) + + saveRDS(mergedClusters[genes.names.test], + file.path(testsDir, "cluster_data_merged.RDS")) + } > > proc.time() user system elapsed 0.203 0.031 0.220
COTAN.Rcheck/tests/spelling.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > if (requireNamespace("spelling", quietly = TRUE)) + spelling::spell_check_test(vignettes = TRUE, error = FALSE, + skip_on_cran = TRUE) NULL > > proc.time() user system elapsed 0.207 0.019 0.216
COTAN.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: aarch64-unknown-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > Sys.setenv(R_TESTS = "") > library(testthat) > library(COTAN) > test_check("COTAN") Setting new log level to 4 Initializing `COTAN` meta-data Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `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: 3.17217755317688 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.00129294395446777 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00840401649475098 Estimating genes' coex Calculate genes' coex elapsed time: 1.03426027297974 Total calculations elapsed time: 4.21613478660583 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 5 genes batches `dispersion` | min: 0.9033203125 | max: 4.6796875 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 7 cells batches 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 `dispersion` | min: 1.0362548828125 | max: 4.60986328125 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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 `dispersion` | min: 0.058837890625 | max: 3.528076171875 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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 `dispersion` | min: 0.32879638671875 | max: 4.0302734375 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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 `dispersion` | min: 0.2294921875 | max: 3.8720703125 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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 `dispersion` | min: 0.2637939453125 | max: 3.929443359375 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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 `dispersion` | min: 0.25177001953125 | max: 3.90966796875 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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 `dispersion` | min: 0.25592041015625 | max: 3.91650390625 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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 `dispersion` | min: 0.2545166015625 | max: 3.914306640625 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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 `dispersion` | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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 `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: 3.17831802368164 Calculating genes' coex normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000952482223510742 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00408172607421875 Estimating genes' coex Calculate genes' coex elapsed time: 1.06935286521912 Total calculations elapsed time: 4.25270509719849 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: 3.12515258789062 Calculating cells' coex normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.0009918212890625 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00307202339172363 Estimating cells' coex Calculate cells' coex elapsed time: 1.03337383270264 Total calculations elapsed time: 4.16259026527405 Calculate cells' coex (legacy): DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Running genes' selection: START Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Running genes' selection: START Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE Included 1 genes with GDI below 1.3 Selected 10 genes using HGDI selector Running genes' selection: DONE Running genes' selection: START Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE Selected 5 genes using HGDI selector Running genes' selection: DONE Running genes' selection: 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% [----|----|----|----|----|----|----|----|----|----| **************************************************| Selected 5 genes using HVG_Seurat selector Running genes' selection: DONE Running genes' selection: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Finding variable features for layer data Calculating gene means 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variance to mean ratios 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Running genes' selection: START Given 5 genes as input Running genes' selection: 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 `dispersion` | min: 0.903564453125 | max: 4.679443359375 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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 `dispersion` | min: 0.0655517578125 | max: 3.5439453125 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Estimate `nu`: DONE `nu` change (abs) | max: 0.402649984216273 | median: 0.231868788425666 | mean: 0.231868788425666 `nu` mean: 0.829218804209393 Marginal errors | max: 0.80321315986594 | median 0.677497553540581 | mean: 0.619375430892821 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.3260498046875 | max: 4.026123046875 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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 `dispersion` | min: 0.23040771484375 | max: 3.8736572265625 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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 `dispersion` | min: 0.26348876953125 | max: 3.928955078125 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches Estimate `nu`: DONE `nu` change (abs) | max: 0.0189966206463044 | median: 0.0110199320575908 | mean: 0.0110199320575908 `nu` mean: 1.00797668858871 Marginal errors | max: 0.0317151207459254 | median 0.0262702142278251 | mean: 0.0240886952086962 Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.2518310546875 | max: 3.9097900390625 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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 `dispersion` | min: 0.2559814453125 | max: 3.9166259765625 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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 `dispersion` | min: 0.25445556640625 | max: 3.9140625 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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 `dispersion` | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 1 cells batches 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: 3.07077240943909 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000733137130737305 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00194954872131348 Estimating genes' coex Calculate genes' coex elapsed time: 0.996618270874023 Total calculations elapsed time: 4.07007336616516 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: 3.06337118148804 Calculating cells' coex normalization factor Calculate cells' normalization factor elapsed time: 0.00075984001159668 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00206303596496582 Estimating cells' coex Calculate cells' coex elapsed time: 1.03416728973389 Total calculations elapsed time: 4.10036134719849 Calculate cells' coex (legacy): DONE Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE Calculate genes' partial coex: START Retrieving expected genes' partial contingency table calculating partial NN.. done calculating partial NY..YN..YY.. done Calculating genes' partial coex normalization factor Fraction of genes with very low expected contingency tables: 0.325 Retrieving observed genes' yes/yes partial contingency table calculating partial YY.. done Estimating genes' partial coex Calculate genes' partial coex: DONE Calculate cells' partial coex: START Retrieving expected cells' partial contingency table calculating partial NN.. done calculating partial YN..NY..YY.. done Calculating cells' partial coex normalization factor Fraction of genes with very low expected contingency tables: 0 Retrieving observed cells' yes/yes partial contingency table calculating partial YY.. done Estimating cells' partial coex Calculate cells' partial coex: DONE Asked to drop 2 genes and 0 cells Asked to drop 0 genes and 4 cells Asked to drop 2 genes and 2 cells Attaching package: 'rlang' The following objects are masked from 'package:testthat': is_false, is_null, is_true Genes/cells selection done: dropped [0] genes and [0] cells Working on [10] genes and [20] cells calculating YY.. done calculating YY.. done calculating YN..NY..NN..t().. done Estimate `dispersion`: START Effective number of cores used: 1 Executing 3 genes batches `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: 3.10581922531128 Calculating genes' coex normalization factor Fraction of genes' with very low expected contingency tables: 0.181818181818182 Calculate genes' normalization factor elapsed time: 0.000968456268310547 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0020904541015625 Estimating genes' coex Calculate genes' coex elapsed time: 1.02409172058105 Total calculations elapsed time: 4.13296985626221 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: 3.11519432067871 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000710010528564453 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00202512741088867 Estimating genes' coex Calculate genes' coex elapsed time: 1.042072057724 Total calculations elapsed time: 4.16000151634216 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 `dispersion` | min: 0.903564453125 | max: 4.679443359375 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches 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 `dispersion` | min: 1.037109375 | max: 4.6107177734375 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches 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 `dispersion` | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches 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: 3.09112906455994 Calculating cells' coex normalization factor Fraction of cells' with very low expected contingency tables: 0 Calculate cells' normalization factor elapsed time: 0.000973939895629883 Retrieving observed cells' yes/yes contingency table calculating YY.. done Observed cells' contingency table elapsed time: 0.00205564498901367 Estimating cells' coex Calculate cells' coex elapsed time: 1.04734444618225 Total calculations elapsed time: 4.14150309562683 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 `dispersion` | min: 0.903564453125 | max: 4.679443359375 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches 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 `dispersion` | min: 1.037109375 | max: 4.6107177734375 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches 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 `dispersion` | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10 Estimate `nu`: START Effective number of cores used: 1 Executing 5 cells batches 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: 3.1058235168457 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.000739812850952148 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00212240219116211 Estimating genes' coex Calculate genes' coex elapsed time: 1.11011505126953 Total calculations elapsed time: 4.21880078315735 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 Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: 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 `dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 4.25138115882874 Cotan genes' coex estimation started Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.85053038597107 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0193386077880859 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0521059036254883 Estimating genes' coex Calculate genes' coex elapsed time: 1.03031778335571 Total calculations elapsed time: 4.95229268074036 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.02800869941711 Total elapsed time: 12.3924369812012 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 `dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 4.3401792049408 Cotan genes' coex estimation started Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.85014128684998 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0190205574035645 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0513484477996826 Estimating genes' coex Calculate genes' coex elapsed time: 1.03097200393677 Total calculations elapsed time: 4.95148229598999 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.00017070770264 Total elapsed time: 12.4208481311798 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 Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 `dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 4.30539560317993 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: 3.75266981124878 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0194528102874756 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0513536930084229 Estimating genes' coex Calculate genes' coex elapsed time: 1.04932498931885 Total calculations elapsed time: 4.87280130386353 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.91275310516357 Total elapsed time: 12.3285026550293 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 Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 `dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 4.20076966285706 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: 3.70847868919373 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.018869161605835 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0512571334838867 Estimating genes' coex Calculate genes' coex elapsed time: 1.02650666236877 Total calculations elapsed time: 4.80511164665222 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.83387160301208 Total elapsed time: 12.0971596240997 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 Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 `dispersion` | min: -0.2119140625 | max: 85.5 | % negative: 62.2144112478032 Cotan genes' coex estimation not requested Total elapsed time: 6.15597128868103 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: 3.11358952522278 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0169188976287842 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00789928436279297 Estimating genes' coex Calculate genes' coex elapsed time: 1.01782560348511 Total calculations elapsed time: 4.15623331069946 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: 3.14268946647644 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0170145034790039 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00783348083496094 Estimating genes' coex Calculate genes' coex elapsed time: 1.02872133255005 Total calculations elapsed time: 4.19625878334045 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: 3.17724871635437 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0177233219146729 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.00792837142944336 Estimating genes' coex Calculate genes' coex elapsed time: 1.02365446090698 Total calculations elapsed time: 4.22655487060547 Calculate genes' coex (legacy): DONE Hangling COTAN object with condition: test Using S Calculating S: START Calculating S: DONE calculating PValues: START Get p-values on a set of genes on columns and on a set of genes on rows calculating PValues: DONE Handling genes type: G2 Handling genes type: G3 Initializing `COTAN` meta-data Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells PCA: START PCA: DONE Hierarchical clustering: START Hierarchical clustering: DONE Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Cotan genes' coex estimation not requested Total elapsed time: 11.5114073753357 Saving elaborated data locally at: /home/biocbuild/tmp/RtmpnFtjLL/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 Asked to drop no genes or cells Running genes' selection: 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% [----|----|----|----|----|----|----|----|----|----| **************************************************| Selected 600 genes using HVG_Seurat selector Running genes' selection: DONE Creating Seurat object: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================================================================| 100% PC_ 1 Positive: g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140 g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135 g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128 Negative: g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528 g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583 g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541 PC_ 2 Positive: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087 g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207 g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158 Negative: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539 g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538 g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570 PC_ 3 Positive: g-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 Negative: 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 PC_ 4 Positive: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 Negative: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 PC_ 5 Positive: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237 g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505 g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393 Negative: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578 g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381 g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272 Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1200 Number of edges: 55489 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5973 Number of communities: 4 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 0.8 Creating Seurat object: DONE Creating PDF UMAP in file: /home/biocbuild/tmp/RtmpnFtjLL/test/reclustering/pdf_umap_1.pdf UMAP plot Calculating UMAP: START 08:15:53 UMAP embedding parameters a = 0.9922 b = 1.112 08:15:53 Read 1200 rows and found 40 numeric columns 08:15:53 Using Annoy for neighbor search, n_neighbors = 30 08:15:53 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 08:15:53 Writing NN index file to temp file /home/biocbuild/tmp/RtmpnFtjLL/file159fb628e720b 08:15:53 Searching Annoy index using 1 thread, search_k = 3000 08:15:53 Annoy recall = 100% 08:15:54 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 08:15:57 Initializing from normalized Laplacian + noise (using RSpectra) 08:15:57 Commencing optimization for 500 epochs, with 42618 positive edges 08:15:57 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 08:16:00 Optimization finished Calculating UMAP: DONE UMAP plot Calculating UMAP: START 08:16:00 UMAP embedding parameters a = 0.9922 b = 1.112 08:16:00 Read 1200 rows and found 40 numeric columns 08:16:00 Using Annoy for neighbor search, n_neighbors = 30 08:16:00 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 08:16:00 Writing NN index file to temp file /home/biocbuild/tmp/RtmpnFtjLL/file159fb1664f46f 08:16:00 Searching Annoy index using 1 thread, search_k = 3000 08:16:01 Annoy recall = 100% 08:16:02 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 08:16:04 Initializing from normalized Laplacian + noise (using RSpectra) 08:16:04 Commencing optimization for 500 epochs, with 42618 positive edges 08:16:04 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 08:16:07 Optimization finished Calculating UMAP: 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 `dispersion` | min: -0.038818359375 | max: 11.109375 | % negative: 5 Only analysis elapsed time: 3.61270451545715 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: 3.57678961753845 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0216236114501953 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0411050319671631 Estimating genes' coex Calculate genes' coex elapsed time: 1.12655448913574 Total calculations elapsed time: 4.76607275009155 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.90895676612854 Total elapsed time: 11.7603394985199 Checking uniformity for the cluster '01_0000' with 353 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 Cluster 01_0000's shift to uniformity: -0.01609905640731 class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0.00833333333333333, check.thresholdRank = 0, check.quantileAtRatio = 1.44390094359269, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 353 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 `dispersion` | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5 Only analysis elapsed time: 3.58222031593323 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: 3.53522801399231 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0189824104309082 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0348601341247559 Estimating genes' coex Calculate genes' coex elapsed time: 1.11781430244446 Total calculations elapsed time: 4.70688486099243 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.84228277206421 Total elapsed time: 11.6210660934448 Checking uniformity for the cluster '01_0001' with 321 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 Cluster 01_0001's shift to uniformity: -0.029501740796507 class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0.005, check.thresholdRank = 0, check.quantileAtRatio = 1.43049825920349, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 321 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 `dispersion` | min: -0.054443359375 | max: 104 | % negative: 36.5 Only analysis elapsed time: 3.61109209060669 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: 3.58480739593506 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0196642875671387 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0177404880523682 Estimating genes' coex Calculate genes' coex elapsed time: 1.12363338470459 Total calculations elapsed time: 4.74584555625916 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.84259724617004 Total elapsed time: 11.7228693962097 Checking uniformity for the cluster '01_0002' with 295 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 Cluster 01_0002's shift to uniformity: -0.0675248136510593 class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0, check.thresholdRank = 0, check.quantileAtRatio = 1.39247518634894, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 295 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 `dispersion` | min: -0.0662841796875 | max: 82.5 | % negative: 33.889816360601 Only analysis elapsed time: 3.50102686882019 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: 3.56522250175476 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0207996368408203 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0188524723052979 Estimating genes' coex Calculate genes' coex elapsed time: 1.13117814064026 Total calculations elapsed time: 4.73605275154114 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.89931631088257 Total elapsed time: 11.6264431476593 Checking uniformity for the cluster '01_0003' with 231 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 Cluster 01_0003's shift to uniformity: -0.0869783653733069 class = SimpleGDIUniformityCheck, check.isCheckAbove = FALSE, check.GDIThreshold = 1.46, check.maxRatioBeyond = 0.01, check.maxRankBeyond = 0, check.fractionBeyond = 0, check.thresholdRank = 0, check.quantileAtRatio = 1.37302163462669, check.quantileAtRank = NaN, isUniform = TRUE, clusterSize = 231 cluster 01_0003 is uniform Found 4 uniform and 0 non-uniform clusters Stopping: too few cells left to cluster Unclustered cell left: 0 The final raw clusterization contains [ 4 ] different clusters: 01_0000, 01_0001, 01_0002, 01_0003 Differential Expression Analysis - START * DEA on cluster '1' with 353 cells * DEA on cluster '2' with 321 cells * DEA on cluster '3' with 295 cells * DEA on cluster '4' with 231 cells Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 3, 2 -> 1, 3 -> 2, 4 -> 4 Creating cells' uniform clustering: DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4 Asked to drop 0 genes and 905 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [295] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.054443359375 | max: 104 | % negative: 36.5 Only analysis elapsed time: 3.54391431808472 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: 3.50997114181519 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0191335678100586 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0174722671508789 Estimating genes' coex Calculate genes' coex elapsed time: 1.11560082435608 Total calculations elapsed time: 4.6621778011322 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.78152799606323 Total elapsed time: 11.5670108795166 Checking uniformity for the cluster 'Cluster_2' with 295 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 Cluster Cluster_2's shift to uniformity: -0.00560790972802239 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0416666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.29139209027198, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.035, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.34700400911787, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00833333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.39247518634894, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 5, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.42797622180141, isUniform = TRUE, clusterSize = 295 Differential Expression Analysis - START * DEA on cluster '-1' with 50 cells * DEA on cluster '1' with 321 cells * DEA on cluster '2' with 245 cells * DEA on cluster '3' with 353 cells * DEA on cluster '4' with 231 cells Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 2, 2 -> 1, 3 -> 4, 4 -> 3, -1 -> -1 Applied reordering to clusterization is: 1 -> 2, 2 -> 3, 3 -> 1, 4 -> 4, -1 -> -1 Creating cells' uniform clustering: START In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters 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 `dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 4.4919068813324 Cotan genes' coex estimation started Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.99886512756348 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0199265480041504 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0530266761779785 Estimating genes' coex Calculate genes' coex elapsed time: 1.15129399299622 Total calculations elapsed time: 5.22311234474182 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.34100651741028 Total elapsed time: 13.0810513496399 Running genes' selection: START Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE Included 186 genes with GDI below 1.3 Selected 600 genes using HGDI selector Running genes' selection: DONE Creating Seurat object: START Normalizing layer: counts Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Centering and scaling data matrix | | | 0% | |======================================================================| 100% PC_ 1 Positive: g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140 g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135 g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128 Negative: g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528 g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583 g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541 PC_ 2 Positive: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087 g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207 g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158 Negative: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539 g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538 g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570 PC_ 3 Positive: g-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 Negative: 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 PC_ 4 Positive: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 Negative: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 PC_ 5 Positive: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237 g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505 g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393 Negative: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578 g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381 g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272 Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1200 Number of edges: 55489 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5973 Number of communities: 4 Elapsed time: 0 seconds Used resolution for Seurat clusterization is: 0.8 Creating Seurat object: DONE Using passed in clusterization Creating PDF UMAP in file: /home/biocbuild/tmp/RtmpnFtjLL/test/reclustering/pdf_umap_1.pdf UMAP plot Calculating UMAP: START 08:18:10 UMAP embedding parameters a = 0.9922 b = 1.112 08:18:10 Read 1200 rows and found 40 numeric columns 08:18:10 Using Annoy for neighbor search, n_neighbors = 30 08:18:10 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 08:18:10 Writing NN index file to temp file /home/biocbuild/tmp/RtmpnFtjLL/file159fb5889782a 08:18:10 Searching Annoy index using 1 thread, search_k = 3000 08:18:10 Annoy recall = 100% 08:18:11 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 08:18:14 Initializing from normalized Laplacian + noise (using RSpectra) 08:18:14 Commencing optimization for 500 epochs, with 42618 positive edges 08:18:14 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 08:18:17 Optimization finished Calculating UMAP: DONE UMAP plot Calculating UMAP: START 08:18:17 UMAP embedding parameters a = 0.9922 b = 1.112 08:18:17 Read 1200 rows and found 40 numeric columns 08:18:17 Using Annoy for neighbor search, n_neighbors = 30 08:18:17 Building Annoy index with metric = cosine, n_trees = 50 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 08:18:18 Writing NN index file to temp file /home/biocbuild/tmp/RtmpnFtjLL/file159fb73bd89fd 08:18:18 Searching Annoy index using 1 thread, search_k = 3000 08:18:18 Annoy recall = 100% 08:18:19 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30 08:18:21 Initializing from normalized Laplacian + noise (using RSpectra) 08:18:21 Commencing optimization for 500 epochs, with 42618 positive edges 08:18:21 Using rng type: pcg Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 08:18:25 Optimization finished Calculating UMAP: DONE * 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 `dispersion` | min: -0.0386962890625 | max: 19.40625 | % negative: 6.5 Only analysis elapsed time: 3.83096957206726 Cotan genes' coex estimation started Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.72693109512329 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0194940567016602 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0378689765930176 Estimating genes' coex Calculate genes' coex elapsed time: 1.13146495819092 Total calculations elapsed time: 4.91575908660889 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.05420732498169 Total elapsed time: 12.10688996315 Checking uniformity for the cluster '01_0001' with 600 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 Cluster 01_0001's shift to uniformity: -0.0122560838733174 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0383333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38474391612668, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.035, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42418110276822, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00666666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.45338035249414, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 4, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.51521594648006, isUniform = TRUE, clusterSize = 600 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 `dispersion` | min: -0.032958984375 | max: 10.0859375 | % negative: 3.66666666666667 Only analysis elapsed time: 3.83261823654175 Cotan genes' coex estimation started Calculate genes' coex (legacy): START Retrieving expected genes' contingency table calculating NN.. done calculating NY..YN..YY..t().. done Expected genes' contingency table elapsed time: 3.74753570556641 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0194618701934814 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0426037311553955 Estimating genes' coex Calculate genes' coex elapsed time: 1.12504839897156 Total calculations elapsed time: 4.93464970588684 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.05437064170837 Total elapsed time: 12.1858711242676 Checking uniformity for the cluster '01_0002' with 600 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 Cluster 01_0002's shift to uniformity: -0.020344550553357 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0366666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37665544944664, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42305229982216, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.4378313582807, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 2, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.50182972335853, isUniform = TRUE, clusterSize = 600 cluster 01_0002 is uniform Found 2 uniform and 0 non-uniform clusters Stopping: too few cells left to cluster Unclustered cell left: 0 The final raw clusterization contains [ 2 ] different clusters: 01_0001, 01_0002 Differential Expression Analysis - START * DEA on cluster '1' with 600 cells * DEA on cluster '2' with 600 cells Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Creating cells' uniform clustering: DONE findClustersMarkers - START 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 Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Log Fold Change Analysis - DONE findClustersMarkers - DONE findClustersMarkers - START Differential Expression Analysis - START * DEA on cluster '1' with 321 cells * DEA on cluster '2' with 295 cells * DEA on cluster '3' with 353 cells * DEA on cluster '4' with 231 cells Differential Expression Analysis - DONE 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] "Tested cluster: 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 `dispersion` | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5 Only analysis elapsed time: 3.70146656036377 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: 3.62106275558472 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0227487087249756 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0374722480773926 Estimating genes' coex Calculate genes' coex elapsed time: 1.13315296173096 Total calculations elapsed time: 4.81443667411804 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.93607687950134 Total elapsed time: 11.8880155086517 Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE [1] "Tested cluster: 4" 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 `dispersion` | min: -0.0662841796875 | max: 82.5 | % negative: 33.889816360601 Only analysis elapsed time: 3.5243763923645 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: 3.57499098777771 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0223865509033203 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0201270580291748 Estimating genes' coex Calculate genes' coex elapsed time: 1.14025139808655 Total calculations elapsed time: 4.75775599479675 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.91975545883179 Total elapsed time: 11.7188792228699 Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 `dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 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 `dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Cotan genes' coex estimation not requested Total elapsed time: 7.96701550483704 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-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 Negative: 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 PC_ 3 Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360 g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470 g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317 Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303 g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262 g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241 PC_ 4 Positive: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079 g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228 g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150 Negative: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131 g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366 g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306 PC_ 5 Positive: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578 g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381 g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272 Negative: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237 g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505 g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393 Computing nearest neighbor graph Computing SNN Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 1200 Number of edges: 55881 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.5915 Number of communities: 4 Elapsed time: 0 seconds Clusterizations found: RNA_snn_res.0.8, seurat_clusters Conditions found: orig.ident 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 `dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Cotan genes' coex estimation not requested Total elapsed time: 7.91427707672119 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 `dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 4.59216451644897 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: 4.10636591911316 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0210380554199219 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0538463592529297 Estimating genes' coex Calculate genes' coex elapsed time: 1.12903785705566 Total calculations elapsed time: 5.31028819084167 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.43294143676758 Total elapsed time: 13.2573211193085 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: 6 Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Number of columns (V set - secondary markers): 6 Number of rows (U set): 60 Calculating gene co-expression space - DONE 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 Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 `dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Cotan genes' coex estimation not requested Total elapsed time: 8.08946871757507 Differential Expression Analysis - START * DEA on cluster '1' with 353 cells * DEA on cluster '2' with 221 cells * DEA on cluster '3' with 315 cells * DEA on cluster '4' with 311 cells Differential Expression Analysis - DONE Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' * Analysis of cluster: '3' * Analysis of cluster: '4' Log Fold Change Analysis - DONE clustersDeltaExpression - START Handling cluster '1' with mean UDE 1.43530796540674 Handling cluster '2' with mean UDE 0.640931107489519 Handling cluster '3' with mean UDE 0.546546914955575 Handling cluster '4' with mean UDE 1.22034802329657 clustersDeltaExpression - DONE In group G1 there are 3 detected over 3 genes In group G2 there are 2 detected over 2 genes In group G3 there are 5 detected over 5 genes Merging cells' uniform clustering: START The merge algorithm will use 2 passes Start merging nearest clusters - the main threshold is: 1.297 Start merging nearest clusters: iteration 1 Differential Expression Analysis - START * DEA on cluster '1' with 353 cells * DEA on cluster '2' with 221 cells * DEA on cluster '3' with 315 cells * DEA on cluster '4' with 311 cells Differential Expression Analysis - DONE Updating check results for the 0 already tested pairs to align to new checker 2 new clusters pairs to be tested for merging: c("1", "2") c("3", "4") *1_2-merge Asked to drop 0 genes and 626 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [574] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333 Only analysis elapsed time: 3.92644548416138 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: 3.74812793731689 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0207881927490234 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0433483123779297 Estimating genes' coex Calculate genes' coex elapsed time: 1.13014769554138 Total calculations elapsed time: 4.94241213798523 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.06655287742615 Total elapsed time: 12.2857441902161 Checking uniformity for the cluster '1_2-merge' with 574 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_2-merge, with size 574, is not uniform Cluster 1_2-merge's shift to uniformity: 0.0820221369127558 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.326666666666667, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37902213691276, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.28, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.41724738266282, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0333333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.42971854140312, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 20, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.5067755752749, isUniform = FALSE, clusterSize = 574 Clusters 1 and 2 cannot be merged *3_4-merge Asked to drop 0 genes and 574 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [626] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667 Only analysis elapsed time: 3.82829594612122 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: 3.7805163860321 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0203282833099365 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0395433902740479 Estimating genes' coex Calculate genes' coex elapsed time: 1.12735915184021 Total calculations elapsed time: 4.9677472114563 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.11631321907043 Total elapsed time: 12.1693053245544 Checking uniformity for the cluster '3_4-merge' with 626 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 3_4-merge, with size 626, is not uniform Cluster 3_4-merge's shift to uniformity: 0.0914611744346205 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.248333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.38846117443462, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.218333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.42066795244751, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0366666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.45442688129939, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 22, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.52592182249634, isUniform = FALSE, clusterSize = 626 Clusters 3 and 4 cannot be merged Finished the first batch - no merges were executed Start merging nearest clusters: iteration 2 Differential Expression Analysis - START * DEA on cluster '1' with 353 cells * DEA on cluster '2' with 221 cells * DEA on cluster '3' with 315 cells * DEA on cluster '4' with 311 cells Differential Expression Analysis - DONE Updating check results for the 2 already tested pairs to align to new checker 2 new clusters pairs to be tested for merging: c("2", "3") c("2", "4") *2_3-merge Asked to drop 0 genes and 664 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [536] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.0390625 | max: 12.59375 | % negative: 9.16666666666667 Only analysis elapsed time: 3.74558305740356 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: 3.71548247337341 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0193188190460205 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0290024280548096 Estimating genes' coex Calculate genes' coex elapsed time: 1.12524104118347 Total calculations elapsed time: 4.88904476165771 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.03073954582214 Total elapsed time: 12.0610914230347 Checking uniformity for the cluster '2_3-merge' with 536 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 2_3-merge, with size 536, is not uniform Cluster 2_3-merge's shift to uniformity: 0.102213698003784 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.29, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.39921369800378, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.251666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.45276697088287, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.05, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.49016449535422, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 30, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.54477108741148, isUniform = FALSE, clusterSize = 536 Clusters 2 and 3 cannot be merged *2_4-merge Asked to drop 0 genes and 668 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [532] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.04754638671875 | max: 10.234375 | % negative: 5 Only analysis elapsed time: 3.95919799804688 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: 3.84508562088013 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0216653347015381 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0410113334655762 Estimating genes' coex Calculate genes' coex elapsed time: 1.15578150749207 Total calculations elapsed time: 5.06354379653931 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.22563171386719 Total elapsed time: 12.5203905105591 Checking uniformity for the cluster '2_4-merge' with 532 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 2_4-merge, with size 532, is not uniform Cluster 2_4-merge's shift to uniformity: 0.213129217682233 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.39, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.51012921768223, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.361666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.55599610798341, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.181666666666667, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.59088431608469, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 109, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.68475283375668, isUniform = FALSE, clusterSize = 532 Clusters 2 and 4 cannot be merged No clusters will be merged None of the remaining tested cluster pairs could be merged Executed all merges for threshold 1.297 out of 4 checks Start merging nearest clusters - the main threshold is: 1.397 Start merging nearest clusters: iteration 3 Differential Expression Analysis - START * DEA on cluster '1' with 353 cells * DEA on cluster '2' with 221 cells * DEA on cluster '3' with 315 cells * DEA on cluster '4' with 311 cells Differential Expression Analysis - DONE Updating check results for the 4 already tested pairs to align to new checker 2 new clusters pairs to be tested for merging: c("1", "3") c("1", "4") *1_3-merge Asked to drop 0 genes and 532 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [668] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.046630859375 | max: 9.03515625 | % negative: 1.33333333333333 Only analysis elapsed time: 4.05221843719482 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: 3.74287891387939 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0191173553466797 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0422923564910889 Estimating genes' coex Calculate genes' coex elapsed time: 1.11840677261353 Total calculations elapsed time: 4.92269539833069 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.04352593421936 Total elapsed time: 12.3921325206757 Checking uniformity for the cluster '1_3-merge' with 668 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_3-merge, with size 668, is not uniform Cluster 1_3-merge's shift to uniformity: 0.177923707405291 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.33, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.57492370740529, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.31, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.6368755707341, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.128333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.65704996173771, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 77, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.68881338289976, isUniform = FALSE, clusterSize = 668 Clusters 1 and 3 cannot be merged *1_4-merge Asked to drop 0 genes and 536 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [664] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.0164794921875 | max: 5.5595703125 | % negative: 0.166666666666667 Only analysis elapsed time: 4.06129670143127 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: 3.81850218772888 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0211982727050781 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0503058433532715 Estimating genes' coex Calculate genes' coex elapsed time: 1.15703749656677 Total calculations elapsed time: 5.047043800354 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.19043612480164 Total elapsed time: 12.5253231525421 Checking uniformity for the cluster '1_4-merge' with 664 cells Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE GDI plot Removed 0 low GDI genes (such as the fully-expressed) in GDI plot Cluster 1_4-merge, with size 664, is not uniform Cluster 1_4-merge's shift to uniformity: 0.138277355686155 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.348333333333333, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.53527735568615, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.316666666666667, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.55951216335001, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0983333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.5910569684761, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 59, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.64605433203112, isUniform = FALSE, clusterSize = 664 Clusters 1 and 4 cannot be merged Clusters 2 and 1 will be merged Clusters 3 and 4 will be merged Executed 2 merges Start merging nearest clusters: iteration 4 Differential Expression Analysis - START * DEA on cluster '1_2-merge' with 574 cells * DEA on cluster '3_4-merge' with 626 cells Differential Expression Analysis - DONE Updating check results for the 6 already tested pairs to align to new checker 1 new clusters pairs to be tested for merging: c("1_2-merge", "3_4-merge") *1_2-merge_3_4-merge-merge Asked to drop no genes or cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [1200] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: 0.2197265625 | max: 6.08056640625 | % negative: 0 Only analysis elapsed time: 4.74990081787109 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: 4.21432590484619 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0203783512115479 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0531117916107178 Estimating genes' coex Calculate genes' coex elapsed time: 1.17344856262207 Total calculations elapsed time: 5.46126461029053 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.63824391365051 Total elapsed time: 13.7130093574524 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 Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 Cluster 1_2-merge_3_4-merge-merge's shift to uniformity: 0.173174985379327 class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.415, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.57017498537933, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.388333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.61240081401504, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.15, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.64046660675367, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 90, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.66512085964759, isUniform = FALSE, clusterSize = 1200 Clusters 1_2-merge and 3_4-merge cannot be merged No clusters will be merged None of the remaining tested cluster pairs could be merged Executed all merges for threshold 1.397 out of 7 checks The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge Differential Expression Analysis - START * DEA on cluster '1' with 574 cells * DEA on cluster '2' with 626 cells Differential Expression Analysis - DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Merging cells' uniform clustering: DONE Applied reordering to clusterization is: 1 -> 1, 2 -> 2 Log Fold Change Analysis - START * Analysis of cluster: '1' * Analysis of cluster: '2' Log Fold Change Analysis - DONE Asked to drop 0 genes and 626 cells Cotan analysis functions started Genes/cells selection done: dropped [0] genes and [0] cells Working on [600] genes and [574] cells Estimate `dispersion`: START Effective number of cores used: 1 Executing 1 genes batches `dispersion` | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333 Only analysis elapsed time: 3.85085988044739 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: 3.67215609550476 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0212326049804688 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.044074535369873 Estimating genes' coex Calculate genes' coex elapsed time: 1.12512922286987 Total calculations elapsed time: 4.86259245872498 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 5.96537971496582 Total elapsed time: 12.1117718219757 Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE 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 `dispersion` | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667 Only analysis elapsed time: 3.94550943374634 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: 3.75630259513855 Calculating genes' coex normalization factor Calculate genes' normalization factor elapsed time: 0.0217485427856445 Retrieving observed genes' yes/yes contingency table calculating YY.. done Observed genes' contingency table elapsed time: 0.0422072410583496 Estimating genes' coex Calculate genes' coex elapsed time: 1.14810919761658 Total calculations elapsed time: 4.96836757659912 Calculate genes' coex (legacy): DONE Only genes' coex elapsed time: 6.11731338500977 Total elapsed time: 12.2840847969055 Calculate GDI dataframe: START Using S Calculating S: START Calculating S: DONE Calculate `GDI`: START Effective number of cores used: 1 Executing 1 genes batches Calculate `GDI`: DONE Calculate GDI dataframe: DONE [ FAIL 0 | WARN 0 | SKIP 0 | PASS 562 ] > > proc.time() user system elapsed 970.260 5.075 970.149
COTAN.Rcheck/COTAN-Ex.timings
name | user | system | elapsed | |
COTAN_Legacy | 0.000 | 0.002 | 0.003 | |
COTAN_ObjectCreation | 13.787 | 1.475 | 14.744 | |
CalculatingCOEX | 73.777 | 0.236 | 71.592 | |
ClustersList | 0.011 | 0.000 | 0.010 | |
Conversions | 7.854 | 0.028 | 7.897 | |
GenesStatistics | 15.261 | 0.043 | 14.827 | |
HandleMetaData | 0.105 | 0.000 | 0.105 | |
HandlingClusterizations | 58.176 | 0.159 | 57.848 | |
HandlingConditions | 0.151 | 0.000 | 0.151 | |
HeatmapPlots | 47.845 | 0.283 | 46.482 | |
LoggingFunctions | 0.002 | 0.000 | 0.003 | |
ParametersEstimations | 34.354 | 0.208 | 34.632 | |
RawDataCleaning | 7.181 | 0.015 | 7.219 | |
RawDataGetters | 0.092 | 0.009 | 0.100 | |
UniformClusters | 250.703 | 0.709 | 249.103 | |
getColorsVector | 0.001 | 0.000 | 0.002 | |