Galfrè Silvia Giulia
| Snapshot Date: 2025-11-24 13:45 -0500 (Mon, 24 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/COTAN |
| git_branch: RELEASE_3_22 |
| git_last_commit: 9b1bfa0 |
| git_last_commit_date: 2025-10-29 11:14:37 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-27 12:05 -0500 (Thu, 27 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4876 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4656 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4602 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 460/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| COTAN 2.10.0 (landing page) Galfrè Silvia Giulia
| nebbiolo2 | 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 | TIMEOUT | NA | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the COTAN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COTAN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: COTAN |
| Version: 2.10.0 |
| 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_2.10.0.tar.gz |
| StartedAt: 2025-11-25 08:23:33 -0000 (Tue, 25 Nov 2025) |
| EndedAt: 2025-11-25 08:44:51 -0000 (Tue, 25 Nov 2025) |
| EllapsedTime: 1277.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: COTAN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings COTAN_2.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/COTAN.Rcheck’
* using R version 4.5.0 (2025-04-11)
* 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)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘2.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 62.391 0.210 62.427
CalculatingCOEX 48.561 0.287 48.377
HandlingClusterizations 42.943 0.167 43.072
HeatmapPlots 31.326 0.288 31.294
ParametersEstimations 21.272 0.175 21.502
GenesStatistics 9.981 0.028 9.871
COTAN_ObjectCreation 9.080 0.185 9.126
RawDataCleaning 5.353 0.008 5.378
* 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: OK
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’ * installing *source* package ‘COTAN’ ... ** this is package ‘COTAN’ version ‘2.10.0’ ** 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 version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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
>
> outputTestDatasetCreation <-
+ function(testsDir = file.path("tests", "testthat")) {
+ utils::data("test.dataset", package = "COTAN")
+ options(parallelly.fork.enable = TRUE)
+ setLoggingLevel(3L)
+
+ obj <- COTAN(raw = test.dataset)
+ obj <- initializeMetaDataset(objCOTAN = obj, GEO = " ",
+ sequencingMethod = "artificial",
+ sampleCondition = "test")
+
+ obj <- proceedToCoex(objCOTAN = obj, cores = 6L, saveObj = FALSE)
+
+ if (FALSE) {
+ saveRDS(obj, file = file.path(testsDir,"test.COTAN.RDS"))
+ }
+
+ cells.names.test <-
+ getCells(objCOTAN = obj)[c(1L:10L, 591L:610L, 991L:1000L)]
+ genes.names.test <-
+ getGenes(objCOTAN = obj)[c(131L:140L, 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"))
+
+ pcaRaw <- runPCA(x = getRawData(objCOTAN = obj), rank = 10L,
+ BSPARAM = IrlbaParam(), get.rotation = FALSE)[["x"]]
+
+ pca.raw.test <- pcaRaw[genes.names.test, ]
+ saveRDS(pca.raw.test, file.path(testsDir, "pca.raw.test.RDS"))
+
+ dispersion.test <- getDispersion(objCOTAN = obj)[genes.names.test]
+ saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS"))
+
+ raw.norm.test <-
+ getNuNormData(objCOTAN = obj)[genes.names.test, cells.names.test]
+ saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS"))
+
+ coex.test <-
+ getGenesCoex(objCOTAN = obj, genes = genes.names.test, zeroDiagonal = FALSE)
+ saveRDS(coex.test, file.path(testsDir, "coex.test.RDS"))
+
+ lambda.test <- getLambda(objCOTAN = obj)[genes.names.test]
+ saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS"))
+
+ GDI.test <- calculateGDI(objCOTAN = obj)
+ GDI.test <- GDI.test[genes.names.test, ]
+ saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS"))
+
+ nu.test <- getNu(objCOTAN = obj)[cells.names.test]
+ saveRDS(nu.test, file.path(testsDir, "nu.test.RDS"))
+
+ pvalues.test <- calculatePValue(objCOTAN = obj,
+ geneSubsetCol = genes.names.test,
+ geneSubsetRow = genes.names.test)
+ saveRDS(pvalues.test, file.path(testsDir, "pvalues.test.RDS"))
+
+ groupMarkers <- list(G1 = c("g-000010", "g-000020", "g-000138"),
+ G2 = c("g-000300", "g-000330", "g-000660"),
+ G3 = c("g-000510", "g-000530", "g-000550",
+ "g-000570", "g-000590"))
+
+ gcsData <- genesCoexSpace(objCOTAN = obj,
+ primaryMarkers = unlist(groupMarkers),
+ numGenesPerMarker = 11L)
+
+ genes.coex.space.test <- gcsData[["GCS"]]
+ saveRDS(genes.coex.space.test,
+ file.path(testsDir, "genes.coex.space.test.RDS"))
+
+ genesClustersData <-
+ establishGenesClusters(objCOTAN = obj,
+ groupMarkers = groupMarkers,
+ numGenesPerMarker = 11L,
+ kCuts = 6L, distance = "cosine",
+ hclustMethod = "ward.D2")
+
+ pca.genes.clusters.test <- genesClustersData[["pca_clusters"]]
+ saveRDS(pca.genes.clusters.test,
+ file.path(testsDir, "pca.genes.clusters.test.RDS"))
+
+ # Make it a less strict check as it is only for testing
+ checker <- new("AdvancedGDIUniformityCheck")
+ checker <- shiftCheckerThresholds(checker, 0.1)
+
+ initialResolution <- 1.3
+ splitData <- cellsUniformClustering(objCOTAN = obj,
+ checker = checker,
+ initialResolution = initialResolution,
+ useCoexEigen = TRUE,
+ dataMethod = "LL",
+ numReducedComp = 50L,
+ cores = 6L, optimizeForSpeed = TRUE,
+ deviceStr = "cuda", saveObj = FALSE)
+
+ split.clusters.test <- splitData[["clusters"]]
+ saveRDS(split.clusters.test,
+ file = file.path(testsDir, "split.clusters.test.RDS"))
+
+ test.dataset.clusters1 <- split.clusters.test
+ save(test.dataset.clusters1, compress = TRUE,
+ file = file.path("data", "test.dataset.clusters1.rda"))
+
+ obj <- addClusterization(objCOTAN = obj,
+ clName = "split",
+ clusters = splitData[["clusters"]],
+ coexDF = splitData[["coex"]])
+
+ coex.clusters.test <- splitData[["coex"]][genes.names.test, ]
+ saveRDS(coex.clusters.test, file.path(testsDir, "coex.clusters.test.RDS"))
+
+ pvalDF <- pValueFromDEA(splitData[["coex"]],
+ getNumCells(objCOTAN = obj),
+ adjustmentMethod = "none")
+
+ pvalues.clusters.test <- pvalDF[genes.names.test, ]
+ saveRDS(pvalues.clusters.test,
+ file.path(testsDir, "pvalues.clusters.test.RDS"))
+
+ mergedData <- mergeUniformCellsClusters(objCOTAN = obj,
+ clusters = splitData[["clusters"]],
+ checkers = checker,
+ batchSize = 1L,
+ cores = 6L,
+ distance = "cosine",
+ hclustMethod = "ward.D2",
+ saveObj = FALSE)
+
+ merge.clusters.test <- mergedData[["clusters"]]
+ saveRDS(merge.clusters.test,
+ file = file.path(testsDir, "merge.clusters.test.RDS"))
+
+ test.dataset.clusters2 <- merge.clusters.test
+ save(test.dataset.clusters2, compress = TRUE,
+ file = file.path("data", "test.dataset.clusters2.rda"))
+
+ obj <- addClusterization(objCOTAN = obj,
+ clName = "merge",
+ clusters = mergedData[["clusters"]],
+ coexDF = mergedData[["coex"]])
+ }
>
> proc.time()
user system elapsed
0.200 0.038 0.222
COTAN.Rcheck/tests/spelling.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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)
All Done!
>
> proc.time()
user system elapsed
0.206 0.029 0.224
COTAN.Rcheck/tests/testthat.Rout
R version 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
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)
> library(zeallot)
> 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
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.64500761032104
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.46319723129272
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000734806060791016
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00871825218200684
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.805928468704224
Total calculations elapsed time: 3.27857875823975
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
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 4 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 4.94965696334839
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 7 cells batches
Total calculations elapsed time: 0.825952053070068
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75595238095238 | median: 1.07156808035714 | mean: 1.07156808035714
Estimate `dispersion`/`nu`: START
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.5858211517334
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03734183779544 | max: 4.61112297272667 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.838697910308838
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0295487661210321 | median: 0.016072261901129 | mean: 0.016072261901129
`nu` mean: 1.69786080481514
Marginal errors | max: 1.95799528048 | median 1.32268477389029 | mean: 1.33563364783916
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.66333055496216
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.0585450475968788 | max: 3.52739274166646 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.754313945770264
Estimate `nu`: DONE
`nu` change (abs) | max: 0.417150556912302 | median: 0.240156504520849 | mean: 0.240156504520849
`nu` mean: 0.823005947608547
Marginal errors | max: 0.837672524335755 | median 0.704691669139065 | mean: 0.646575831699997
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.60512018203735
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.328845855849147 | max: 4.03031691940854 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.827348232269287
Estimate `nu`: DONE
`nu` change (abs) | max: 0.164439840041 | median: 0.0957105992188852 | mean: 0.0957105992188852
`nu` mean: 1.06872924082212
Marginal errors | max: 0.260109847946692 | median 0.21392791155499 | mean: 0.197565106613054
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.6645405292511
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.229469002841045 | max: 3.87206403670079 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.84464693069458
Estimate `nu`: DONE
`nu` change (abs) | max: 0.05539667181205 | median: 0.0321044921874999 | mean: 0.0321044921874999
`nu` mean: 0.97670782037545
Marginal errors | max: 0.095347789718808 | median 0.0796003827042702 | mean: 0.0725509735761708
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.60305571556091
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.263830434255107 | max: 3.92953043775907 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.820634603500366
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0196209299693411 | median: 0.0114037947200925 | mean: 0.0114037947200925
`nu` mean: 1.00821713524925
Marginal errors | max: 0.0329495161656741 | median 0.0273479725376324 | mean: 0.025029675152131
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.73020029067993
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.251734659898779 | max: 3.9096133246649 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.831424474716187
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0069104540740097 | median: 0.0040109538496062 | mean: 0.0040109538496062
`nu` mean: 0.997100499775596
Marginal errors | max: 0.0116950057438405 | median 0.00972280144873849 | mean: 0.00889105008777538
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.69319152832031
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.256009779031907 | max: 3.91667271750655 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.84499979019165
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00251004753849005 | median: 0.00146484374999994 | mean: 0.00146484374999994
`nu` mean: 1.00104520378849
Marginal errors | max: 0.00430755646112857 | median 0.00358203399504298 | mean: 0.00327684342604062
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.63538265228271
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.254429717857093 | max: 3.91406908073254 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.86847972869873
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00104629156456748 | median: 0.000592910406456731 | mean: 0.000592910406456731
`nu` mean: 0.999546618841889
Marginal errors | max: 0.00162038706091039 | median 0.00134441676098973 | mean: 0.00123030512553282
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.63957333564758
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.255022049769696 | max: 3.91504587939868 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.840915679931641
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000418450901304768 | median: 0.000244140625000028 | mean: 0.000244140625000028
`nu` mean: 1.0001743102763
Marginal errors | max: 0.00071569233034019 | median 0.000597297218559056 | mean: 0.00054590699507937
Total calculations elapsed time: 44.380181312561
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
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.66267561912537
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % 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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.43606734275818
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.0010838508605957
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00457072257995605
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.873088836669922
Total calculations elapsed time: 3.31481075286865
Calculate genes' COEX (legacy): DONE
Calculate cells' COEX (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 2.37757015228271
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000969409942626953
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00302338600158691
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.816236257553101
Total calculations elapsed time: 3.19779920578003
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
Total calculations elapsed time: 0.0128610134124756
Calculate `GDI`: DONE
Total calculations elapsed time: 2.53705883026123
Calculate GDI dataframe: 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
Total calculations elapsed time: 0.00446534156799316
Calculate `GDI`: DONE
Total calculations elapsed time: 2.65618443489075
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
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Running genes' selection: START
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
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 1.68366074562073
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Included 1 genes with GDI below 1.3
Selected 10 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 1.72676229476929
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Running genes' selection: START
Selected 8 genes using HGDI selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 1.79542112350464
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
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 8 genes using HVG_Seurat selector
Running genes' selection: DONE
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 2.7695677280426
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 2.5093400478363
Elaborating Reduced dimensionality Data Matrix - DONE
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 2.37245869636536
Elaborating Reduced dimensionality Data Matrix - 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
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.58866214752197
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.774689435958862
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 1.735699617106 | median 1.37997441333659 | mean: 1.32181397451301
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.65675568580627
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.0655494303592343 | max: 3.54400580804152 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.787784576416016
Estimate `nu`: DONE
`nu` change (abs) | max: 0.402649984216273 | median: 0.231868788425666 | mean: 0.231868788425666
`nu` mean: 0.829218804209393
Marginal errors | max: 0.803248939260364 | median 0.677504196374571 | mean: 0.619386446933351
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.67499589920044
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.326019058449519 | max: 4.02612397202046 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.82705283164978
Estimate `nu`: DONE
`nu` change (abs) | max: 0.158004893526231 | median: 0.0919692884670312 | mean: 0.0919692884670312
`nu` mean: 1.0660356050592
Marginal errors | max: 0.25067700287536 | median 0.206241644985115 | mean: 0.190402167377958
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.61454343795776
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.230397316576369 | max: 3.87365659194104 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.827198028564453
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0532774732102337 | median: 0.0308837890624999 | mean: 0.0308837890624999
`nu` mean: 0.977606315852266
Marginal errors | max: 0.0916920322976189 | median 0.0765360853958175 | mean: 0.0697673030094085
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.54497361183167
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.263457616228195 | max: 3.928924407347 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.767595529556274
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0187878665732679 | median: 0.0109155550210726 | mean: 0.0109155550210726
`nu` mean: 1.0078723115522
Marginal errors | max: 0.0315207323253404 | median 0.0261635598193228 | mean: 0.0239435763640456
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.70612454414368
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.251890641847533 | max: 3.90987172241566 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.891570806503296
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00649137083358098 | median: 0.00376680890457393 | mean: 0.00376680890457393
`nu` mean: 0.997275438070993
Marginal errors | max: 0.0109748802265024 | median 0.00912386940474796 | mean: 0.00834350038184244
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.68114495277405
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.255902752363649 | max: 3.91649655995187 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.78490161895752
Estimate `nu`: DONE
`nu` change (abs) | max: 0.00230094227000666 | median: 0.00132529141000018 | mean: 0.00132529141000018
`nu` mean: 1.00097565086001
Marginal errors | max: 0.00376864912836616 | median 0.00313421412286008 | mean: 0.00286709489297579
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.62299275398254
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.254520292119112 | max: 3.91421850264948 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.816583633422852
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000837013154366462 | median: 0.000488281250000028 | mean: 0.000488281250000028
`nu` mean: 0.999651268095634
Marginal errors | max: 0.00144055320514802 | median 0.00119489364392944 | mean: 0.00109355439757213
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 1.72243595123291
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.255046800817986 | max: 3.9150866760965 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 1 cells batches
Total calculations elapsed time: 0.840445041656494
Estimate `nu`: DONE
`nu` change (abs) | max: 0.000418448154490214 | median: 0.000244140624999917 | mean: 0.000244140624999917
`nu` mean: 1.00017430752949
Marginal errors | max: 0.000715683388516908 | median 0.0005972847342397 | mean: 0.00054589991652243
Total calculations elapsed time: 44.5049524307251
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.59411692619324
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000696897506713867
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00181150436401367
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.84902024269104
Total calculations elapsed time: 3.445645570755
Calculate genes' COEX (legacy): DONE
Calculate cells' COEX (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 2.73200273513794
Calculating cells' COEX normalization factor
Calculate cells' normalization factor elapsed time: 0.000790596008300781
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00207805633544922
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.928016185760498
Total calculations elapsed time: 3.66288757324219
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
Total calculations elapsed time: 0.00492715835571289
Calculate `GDI`: DONE
Total calculations elapsed time: 2.86965370178223
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
Total calculations elapsed time: 6.90321278572083
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
Total calculations elapsed time: 7.11762261390686
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
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.16258502006531
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
calculating NN.. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.44197106361389
Calculating genes' COEX normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000902652740478516
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00187158584594727
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.789931297302246
Total calculations elapsed time: 3.23467659950256
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.40291833877563
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00067138671875
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00188970565795898
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.770512819290161
Total calculations elapsed time: 3.1759922504425
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
Total calculations elapsed time: 6.41113018989563
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
Total calculations elapsed time: 6.41095662117004
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
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.3366870880127
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.794806480407715
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 0.255290533439036 | median 0.080731376500534 | mean: 0.101968565509112
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.22801899909973
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03709166563768 | max: 4.61069655774133 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.820387125015259
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00330148418741594 | median 0.00111713187082163 | mean: 0.00132007186542964
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.27878928184509
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03887279473672 | max: 4.60974134092906 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.800916910171509
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median: 0 | mean: 0
`nu` mean: 1.69735147626627
Marginal errors | max: 5.14174422185931e-05 | median 1.6818224857218e-07 | mean: 5.57649710835051e-06
Total calculations elapsed time: 19.8219082355499
Estimate `dispersion`/`nu`: DONE
calculating NN.. done
calculating NN.. done
calculating YN..NY..YY..t().. done
Calculate cells' COEX (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 2.44211077690125
Calculating cells' COEX normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000880002975463867
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00192070007324219
Estimating cells' COEX
Calculate cells' COEX elapsed time: 0.825177431106567
Total calculations elapsed time: 3.27008891105652
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
Total calculations elapsed time: 6.5209367275238
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
Total calculations elapsed time: 6.53204488754272
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
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.35846972465515
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 0.903596292963576 | max: 4.67949426963453 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.792292356491089
Estimate `nu`: DONE
`nu` change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014
`nu` mean: 1.68489292689732
Marginal errors | max: 0.255290533439036 | median 0.080731376500534 | mean: 0.101968565509112
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.35483074188232
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03709166563768 | max: 4.61069655774133 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.866785764694214
Estimate `nu`: DONE
`nu` change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011
`nu` mean: 1.69735147626627
Marginal errors | max: 0.00330148418741594 | median 0.00111713187082163 | mean: 0.00132007186542964
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 3 genes batches
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Parallel dispersion Newton-Raphson: used up to 5 iterations
Total calculations elapsed time: 3.32671046257019
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: 1.03887279473672 | max: 4.60974134092906 | % negative: 10
Estimate `nu`: START
Effective number of cores used: 1
Executing 5 cells batches
Total calculations elapsed time: 0.927026748657227
Estimate `nu`: DONE
`nu` change (abs) | max: 0 | median: 0 | mean: 0
`nu` mean: 1.69735147626627
Marginal errors | max: 5.14174422185931e-05 | median 1.6818224857218e-07 | mean: 5.57649710835051e-06
Total calculations elapsed time: 20.1750612258911
Estimate `dispersion`/`nu`: DONE
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.53221988677979
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.000860452651977539
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00227618217468262
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.836228847503662
Total calculations elapsed time: 3.37158536911011
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
Total calculations elapsed time: 5.79307699203491
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
Total calculations elapsed time: 0.00294804573059082
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
Total calculations elapsed time: 5.52776193618774
Calculating G: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
Total calculations elapsed time: 5.52935075759888
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
Total calculations elapsed time: 0.00422549247741699
Calculate `GDI`: DONE
Total calculations elapsed time: 2.49985194206238
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
Total calculations elapsed time: 5.67985391616821
Calculating G: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00461506843566895
Calculate `GDI`: DONE
Total calculations elapsed time: 8.17631435394287
Calculate GDI dataframe: DONE
Calculate `GDI`: START
Calculating S: START
Calculating S: DONE
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00635242462158203
Calculate `GDI`: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00516343116760254
Calculate `GDI`: DONE
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.856918334960938
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.95171761512756
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.80379247665405
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.65249061584473
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0134916305541992
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0668461322784424
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.838053226470947
Total calculations elapsed time: 3.57088160514832
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.4465856552124
Dataset analysis elapsed time: 8.10729646682739
COTAN dataset analysis: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1000
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.846021175384521
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.85527968406677
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.67618775367737
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.69694638252258
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0135834217071533
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0679159164428711
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.798754930496216
Total calculations elapsed time: 3.57720065116882
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.39101672172546
Dataset analysis elapsed time: 7.91322565078735
COTAN dataset analysis: DONE
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
Total calculations elapsed time: 0.023874044418335
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
Total calculations elapsed time: 0.0321934223175049
Calculate `GDI`: DONE
Total calculations elapsed time: 2.55664825439453
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1000
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.800435066223145
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.84741568565369
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.68851780891418
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.69061994552612
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0134124755859375
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0652942657470703
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.780011177062988
Total calculations elapsed time: 3.54933786392212
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.34865283966064
Dataset analysis elapsed time: 7.83760571479797
COTAN dataset analysis: DONE
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
Total calculations elapsed time: 0.0216419696807861
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
Total calculations elapsed time: 0.0329623222351074
Calculate `GDI`: DONE
Total calculations elapsed time: 2.46854019165039
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1000
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.787873029708862
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.78453302383423
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.55368304252625
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.55844902992249
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.013110876083374
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0644717216491699
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.78646445274353
Total calculations elapsed time: 3.42249608039856
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.25279021263123
Dataset analysis elapsed time: 7.59434628486633
COTAN dataset analysis: DONE
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
Total calculations elapsed time: 0.00722289085388184
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
Total calculations elapsed time: 0.0318019390106201
Calculate `GDI`: DONE
Total calculations elapsed time: 2.47115659713745
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Asked to drop 0 genes and 960 cells
COTAN dataset analysis: START
Asked to drop 83 genes and 0 cells
Genes/cells selection done: dropped [83] genes and [0] cells
Working on [517] genes and [40] cells
Dataset cleaning elapsed time: 0.798200845718384
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.67946410179138
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.267567793681876 | max: 101.923257389521 | % negative: 52.6112185686654
Model parameter estimation elapsed time: 2.50693345069885
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.892879009246826
Dataset analysis elapsed time: 4.19801330566406
COTAN dataset analysis: DONE
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.52792286872864
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0105681419372559
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0120537281036377
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.851547241210938
Total calculations elapsed time: 3.40209197998047
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.50652384757996
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0102498531341553
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0117676258087158
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.793546676635742
Total calculations elapsed time: 3.32208800315857
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.50437211990356
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0103840827941895
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0122504234313965
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.820478916168213
Total calculations elapsed time: 3.34748554229736
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
Total calculations elapsed time: 0.00629472732543945
calculating PValues: DONE
Handling genes type: G2
Handling genes type: G3
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Clean plots: START
PCA: START
PCA: DONE
Hierarchical clustering: START
Hierarchical clustering: DONE
Total calculations elapsed time: 1.98741865158081
Clean plots: DONE
Dataset cleaning elapsed time: 4.57809567451477
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.0634937286377
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 3.00714254379272
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.94235968589783
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0133190155029297
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0672183036804199
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.894509792327881
Total calculations elapsed time: 3.91740679740906
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.83862614631653
Dataset analysis elapsed time: 12.423864364624
COTAN dataset analysis: DONE
Saving elaborated data locally at: /home/biocbuild/tmp/Rtmpu5OXKz/test.cotan.RDS
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 2.74577665328979
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1000
Number of edges: 44886
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.4008
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 1.3
Total calculations elapsed time: 3.93957185745239
Creating new clusterization: DONE
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1000 cells belonging to 0 clusters
Asked to drop no genes or cells
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
Elaborating COEX Eigen Vectors - START
Elaborating COEX Eigen Vectors - DONE
Total calculations elapsed time: 2.7814028263092
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1000
Number of edges: 36652
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.3743
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 1.3
Total calculations elapsed time: 3.85785984992981
Creating new clusterization: DONE
Creating PDF UMAP in file: /home/biocbuild/tmp/Rtmpu5OXKz/test/reclustering/pdf_umap_1.pdf
UMAP plot: START
Calculating UMAP: START
08:40:12 UMAP embedding parameters a = 0.9922 b = 1.112
08:40:12 Read 1000 rows and found 65 numeric columns
08:40:12 Using Annoy for neighbor search, n_neighbors = 30
08:40:12 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:40:12 Writing NN index file to temp file /home/biocbuild/tmp/Rtmpu5OXKz/file2616d85ff850f3
08:40:12 Searching Annoy index using 1 thread, search_k = 3000
08:40:12 Annoy recall = 100%
08:40:13 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
08:40:15 Initializing from normalized Laplacian + noise (using RSpectra)
08:40:15 Commencing optimization for 500 epochs, with 39044 positive edges
08:40:15 Using rng type: pcg
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:40:18 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.92699027061462
UMAP plot: DONE
UMAP plot: START
Calculating UMAP: START
08:40:18 UMAP embedding parameters a = 0.9922 b = 1.112
08:40:18 Read 1000 rows and found 65 numeric columns
08:40:18 Using Annoy for neighbor search, n_neighbors = 30
08:40:18 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:40:19 Writing NN index file to temp file /home/biocbuild/tmp/Rtmpu5OXKz/file2616d871c07781
08:40:19 Searching Annoy index using 1 thread, search_k = 3000
08:40:19 Annoy recall = 100%
08:40:20 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
08:40:21 Initializing from normalized Laplacian + noise (using RSpectra)
08:40:22 Commencing optimization for 500 epochs, with 39044 positive edges
08:40:22 Using rng type: pcg
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:40:24 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.98248195648193
UMAP plot: DONE
* checking uniformity of cluster '0' of 4 clusters
Asked to drop 0 genes and 687 cells
COTAN dataset analysis: START
Asked to drop 43 genes and 0 cells
Genes/cells selection done: dropped [43] genes and [0] cells
Working on [557] genes and [313] cells
Dataset cleaning elapsed time: 0.920477628707886
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 11 iterations
Total calculations elapsed time: 1.98515105247498
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.126565269702225 | max: 788.372048308528 | % negative: 38.5996409335727
Model parameter estimation elapsed time: 2.90639758110046
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.7953143119812
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0117959976196289
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0299191474914551
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.890090227127075
Total calculations elapsed time: 3.72711968421936
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.59757399559021
Dataset analysis elapsed time: 8.42444920539856
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0000' with 313 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
Total calculations elapsed time: 0.0306272506713867
Calculate `GDI`: DONE
Total calculations elapsed time: 2.78290987014771
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0538363456726074
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0000, with size 313, is uniform
Cluster 01_0000's shift to uniformity: -0.0175178017151116
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0412926391382406, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37948219828489, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.0323159784560144, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.43089123341142, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00179533213644524, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.44383613651627, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 1, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.47612588512219, isUniform = TRUE, clusterSize = 313
cluster 01_0000 is uniform
* checking uniformity of cluster '1' of 4 clusters
Asked to drop 0 genes and 743 cells
COTAN dataset analysis: START
Asked to drop 51 genes and 0 cells
Genes/cells selection done: dropped [51] genes and [0] cells
Working on [549] genes and [257] cells
Dataset cleaning elapsed time: 0.905565977096558
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 10 iterations
Total calculations elapsed time: 1.73950171470642
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998
Model parameter estimation elapsed time: 2.58372902870178
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.63007187843323
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0110490322113037
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0264768600463867
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.878874540328979
Total calculations elapsed time: 3.5464723110199
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.43514490127563
Dataset analysis elapsed time: 7.92443990707397
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0001' with 257 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
Total calculations elapsed time: 0.0290849208831787
Calculate `GDI`: DONE
Total calculations elapsed time: 2.65020442008972
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0535013675689697
Clean plots: DONE
GDI plot
Removed 1 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 257, is uniform
Cluster 01_0001's shift to uniformity: -0.0466523594846466
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00910746812386157, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35034764051535, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00728597449908925, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37278730407695, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38664163146848, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.45240567481125, isUniform = TRUE, clusterSize = 257
cluster 01_0001 is uniform
* checking uniformity of cluster '2' of 4 clusters
Asked to drop 0 genes and 758 cells
COTAN dataset analysis: START
Asked to drop 77 genes and 0 cells
Genes/cells selection done: dropped [77] genes and [0] cells
Working on [523] genes and [242] cells
Dataset cleaning elapsed time: 0.817822217941284
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.77191233634949
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.166254045792573 | max: 224.924342782861 | % negative: 42.6386233269598
Model parameter estimation elapsed time: 2.640873670578
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.64140343666077
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0102946758270264
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0243089199066162
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.860171318054199
Total calculations elapsed time: 3.53617835044861
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.39934325218201
Dataset analysis elapsed time: 7.85803914070129
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0002' with 242 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
Total calculations elapsed time: 0.0271785259246826
Calculate `GDI`: DONE
Total calculations elapsed time: 2.64301013946533
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0526101589202881
Clean plots: DONE
GDI plot
Removed 2 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 242, is uniform
Cluster 01_0002's shift to uniformity: -0.0473527936300073
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00764818355640535, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.34964720636999, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00764818355640535, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37472946305403, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38771313919655, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.43097703442028, isUniform = TRUE, clusterSize = 242
cluster 01_0002 is uniform
* checking uniformity of cluster '3' of 4 clusters
Asked to drop 0 genes and 812 cells
COTAN dataset analysis: START
Asked to drop 79 genes and 0 cells
Genes/cells selection done: dropped [79] genes and [0] cells
Working on [521] genes and [188] cells
Dataset cleaning elapsed time: 0.901740789413452
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 6 iterations
Total calculations elapsed time: 1.76080632209778
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.210007411487223 | max: 67.8701314818728 | % negative: 45.6813819577735
Model parameter estimation elapsed time: 2.64121198654175
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.63052415847778
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.00962734222412109
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0214622020721436
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.855331182479858
Total calculations elapsed time: 3.51694488525391
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.44952917098999
Dataset analysis elapsed time: 7.99248194694519
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0003' with 188 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
Total calculations elapsed time: 0.0263693332672119
Calculate `GDI`: DONE
Total calculations elapsed time: 2.61296629905701
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0506227016448975
Clean plots: DONE
GDI plot
Removed 4 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0003, with size 188, is uniform
Cluster 01_0003's shift to uniformity: -0.0672912272436044
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00383877159309021, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.3297087727564, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00191938579654511, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.35752445041521, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.37495297633957, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.4014884302523, isUniform = TRUE, clusterSize = 188
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 313 cells
* DEA on cluster '2' with 257 cells
* DEA on cluster '3' with 242 cells
* DEA on cluster '4' with 188 cells
Total calculations elapsed time: 0.0483627319335938
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 3, 2 -> 1, 3 -> 2, 4 -> 4
Total calculations elapsed time: 76.3255417346954
Creating cells' uniform clustering: DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4
Asked to drop 0 genes and 812 cells
COTAN dataset analysis: START
Asked to drop 79 genes and 0 cells
Genes/cells selection done: dropped [79] genes and [0] cells
Working on [521] genes and [188] cells
Dataset cleaning elapsed time: 0.865225791931152
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 6 iterations
Total calculations elapsed time: 1.75111365318298
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.210007411487223 | max: 67.8701314818728 | % negative: 45.6813819577735
Model parameter estimation elapsed time: 2.62677121162415
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.64113545417786
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0104408264160156
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0221080780029297
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.877001762390137
Total calculations elapsed time: 3.55068612098694
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.41481804847717
Dataset analysis elapsed time: 7.90681505203247
COTAN dataset analysis: DONE
Checking uniformity for the cluster 'Cluster_4' with 188 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
Total calculations elapsed time: 0.0271987915039062
Calculate `GDI`: DONE
Total calculations elapsed time: 2.66276264190674
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0523841381072998
Clean plots: DONE
GDI plot
Removed 4 low GDI genes (such as the fully-expressed) in GDI plot
Cluster Cluster_4, with size 188, is uniform
Cluster Cluster_4's shift to uniformity: -0.0672912272436044
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00383877159309021, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.3297087727564, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00191938579654511, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.35752445041521, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.37495297633957, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.4014884302523, isUniform = TRUE, clusterSize = 188
Differential Expression Analysis - START
* DEA on cluster '-1' with 50 cells
* DEA on cluster '1' with 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 280 cells
* DEA on cluster '4' with 171 cells
Total calculations elapsed time: 0.0492222309112549
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 4, 2 -> 3, 3 -> 2, 4 -> 1, -1 -> -1
Applied reordering to clusterization is:
1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4, -1 -> -1
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1000 cells belonging to 0 clusters
Asked to drop no genes or cells
Creating new clusterization: START
Elaborating Reduced dimensionality Data Matrix - START
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
Elaborating PCA - START
Elaborating PCA - DONE
Total calculations elapsed time: 3.31955242156982
Elaborating Reduced dimensionality Data Matrix - DONE
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1000
Number of edges: 67288
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.3650
Number of communities: 5
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 1.3
Total calculations elapsed time: 4.42835474014282
Creating new clusterization: DONE
Using passed in clusterization
Creating PDF UMAP in file: /home/biocbuild/tmp/Rtmpu5OXKz/test/reclustering/pdf_umap_1.pdf
UMAP plot: START
Calculating UMAP: START
08:41:44 UMAP embedding parameters a = 0.9922 b = 1.112
08:41:44 Read 1000 rows and found 40 numeric columns
08:41:44 Using Annoy for neighbor search, n_neighbors = 30
08:41:44 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:41:44 Writing NN index file to temp file /home/biocbuild/tmp/Rtmpu5OXKz/file2616d817d6e9df
08:41:44 Searching Annoy index using 1 thread, search_k = 3000
08:41:44 Annoy recall = 100%
08:41:45 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
08:41:47 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1
08:41:47 Using 'irlba' for PCA
08:41:47 PCA: 2 components explained 36.15% variance
08:41:47 Scaling init to sdev = 1
08:41:47 Commencing optimization for 500 epochs, with 41630 positive edges
08:41:47 Using rng type: pcg
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:41:50 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 5.9161262512207
UMAP plot: DONE
UMAP plot: START
Calculating UMAP: START
08:41:50 UMAP embedding parameters a = 0.9922 b = 1.112
08:41:50 Read 1000 rows and found 40 numeric columns
08:41:50 Using Annoy for neighbor search, n_neighbors = 30
08:41:50 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:41:50 Writing NN index file to temp file /home/biocbuild/tmp/Rtmpu5OXKz/file2616d85680d309
08:41:50 Searching Annoy index using 1 thread, search_k = 3000
08:41:50 Annoy recall = 100%
08:41:51 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
08:41:53 Found 2 connected components, falling back to 'spca' initialization with init_sdev = 1
08:41:53 Using 'irlba' for PCA
08:41:53 PCA: 2 components explained 36.15% variance
08:41:53 Scaling init to sdev = 1
08:41:53 Commencing optimization for 500 epochs, with 41630 positive edges
08:41:53 Using rng type: pcg
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
08:41:56 Optimization finished
Calculating UMAP: DONE
Total calculations elapsed time: 6.02703547477722
UMAP plot: DONE
* checking uniformity of cluster '1' of 2 clusters
Asked to drop 0 genes and 500 cells
COTAN dataset analysis: START
Asked to drop 38 genes and 0 cells
Genes/cells selection done: dropped [38] genes and [0] cells
Working on [562] genes and [500] cells
Dataset cleaning elapsed time: 0.86084508895874
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.80338931083679
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.108871643378045 | max: 295.971778839086 | % negative: 35.0533807829181
Model parameter estimation elapsed time: 2.7081835269928
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.85913324356079
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0120458602905273
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.038055419921875
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.934298038482666
Total calculations elapsed time: 3.84353256225586
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.76113939285278
Dataset analysis elapsed time: 8.33016800880432
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0001' with 500 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
Total calculations elapsed time: 0.0312144756317139
Calculate `GDI`: DONE
Total calculations elapsed time: 2.68370962142944
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0536587238311768
Clean plots: DONE
GDI plot
Removed 2 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 500, is uniform
Cluster 01_0001's shift to uniformity: -0.0417301990664185
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.0124555160142349, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35526980093358, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00889679715302491, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.38536328181495, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.40346106115496, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.42565794715039, isUniform = TRUE, clusterSize = 500
cluster 01_0001 is uniform
* checking uniformity of cluster '2' of 2 clusters
Asked to drop 0 genes and 500 cells
COTAN dataset analysis: START
Asked to drop 44 genes and 0 cells
Genes/cells selection done: dropped [44] genes and [0] cells
Working on [556] genes and [500] cells
Dataset cleaning elapsed time: 0.891474008560181
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.89357566833496
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0636486786621688 | max: 141.389145035675 | % negative: 36.1510791366906
Model parameter estimation elapsed time: 2.75074100494385
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.75168132781982
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0113804340362549
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0367748737335205
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.883605241775513
Total calculations elapsed time: 3.68344187736511
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.58182144165039
Dataset analysis elapsed time: 8.22403645515442
COTAN dataset analysis: DONE
Checking uniformity for the cluster '01_0002' with 500 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
Total calculations elapsed time: 0.0307636260986328
Calculate `GDI`: DONE
Total calculations elapsed time: 2.71322965621948
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0547878742218018
Clean plots: DONE
GDI plot
Removed 2 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 500, is uniform
Cluster 01_0002's shift to uniformity: -0.0413872276843519
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.00719424460431655, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35561277231565, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.00359712230215827, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37204026755189, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38757136821537, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 0, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.40876953414112, isUniform = TRUE, clusterSize = 500
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 500 cells
* DEA on cluster '2' with 500 cells
Total calculations elapsed time: 0.0425260066986084
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Total calculations elapsed time: 47.9950792789459
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'
Total calculations elapsed time: 3.59165287017822
Log Fold Change Analysis - DONE
Total calculations elapsed time: 3.60768866539001
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'
Total calculations elapsed time: 3.44392085075378
Log Fold Change Analysis - DONE
Total calculations elapsed time: 3.458820104599
findClustersMarkers - DONE
findClustersMarkers - START
Differential Expression Analysis - START
* DEA on cluster '1' with 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 313 cells
* DEA on cluster '4' with 188 cells
Total calculations elapsed time: 0.0435032844543457
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'
Total calculations elapsed time: 3.47854471206665
Log Fold Change Analysis - DONE
Total calculations elapsed time: 3.53502821922302
findClustersMarkers - DONE
[1] "Tested cluster: 1"
Asked to drop 0 genes and 743 cells
COTAN dataset analysis: START
Asked to drop 51 genes and 0 cells
Genes/cells selection done: dropped [51] genes and [0] cells
Working on [549] genes and [257] cells
Dataset cleaning elapsed time: 0.891881704330444
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 10 iterations
Total calculations elapsed time: 1.80741858482361
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.112503099391263 | max: 646.681464270838 | % negative: 40.8014571948998
Model parameter estimation elapsed time: 2.60970830917358
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.62537550926208
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0110280513763428
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0262250900268555
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.826947450637817
Total calculations elapsed time: 3.4895761013031
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.34053254127502
Dataset analysis elapsed time: 7.84212255477905
COTAN dataset analysis: 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
Total calculations elapsed time: 0.0290427207946777
Calculate `GDI`: DONE
Total calculations elapsed time: 2.65795731544495
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 [1000] cells
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.04083251953125
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.906385898590088
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.00195574760437
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.85962271690369
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.842347145080566
Dataset analysis elapsed time: 4.60835576057434
COTAN dataset analysis: DONE
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-000397, g-000525, g-000460, g-000458, g-000535, g-000217, g-000194, g-000497, g-000432, g-000383
g-000318, g-000486, g-000464, g-000588, g-000549, g-000368, g-000252, g-000151, g-000209, g-000538
g-000325, g-000514, g-000524, g-000244, g-000320, g-000201, g-000499, g-000309, g-000290, g-000483
Negative: g-000415, g-000506, g-000496, g-000579, g-000572, g-000421, g-000455, g-000328, g-000178, g-000567
g-000405, g-000296, g-000387, g-000501, g-000493, g-000481, g-000343, g-000528, g-000551, g-000414
g-000367, g-000594, g-000159, g-000517, g-000574, g-000229, g-000222, g-000533, g-000243, g-000306
PC_ 2
Positive: g-000141, g-000093, g-000089, g-000033, g-000123, g-000557, g-000330, g-000156, g-000142, g-000095
g-000061, g-000235, g-000032, g-000186, g-000056, g-000259, g-000027, g-000041, g-000333, g-000386
g-000009, g-000395, g-000048, g-000116, g-000340, g-000418, g-000035, g-000332, g-000086, g-000040
Negative: g-000088, g-000158, g-000255, g-000115, g-000054, g-000472, g-000554, g-000391, g-000253, g-000226
g-000051, g-000147, g-000541, g-000077, g-000224, g-000194, g-000290, g-000293, g-000313, g-000118
g-000121, g-000220, g-000467, g-000500, g-000341, g-000039, g-000091, g-000249, g-000426, g-000288
PC_ 3
Positive: g-000126, g-000083, g-000086, g-000117, g-000130, g-000010, g-000498, g-000333, g-000047, g-000179
g-000340, g-000035, g-000531, g-000140, g-000527, g-000049, g-000316, g-000031, g-000014, g-000073
g-000218, g-000445, g-000129, g-000175, g-000105, g-000581, g-000404, g-000025, g-000266, g-000354
Negative: g-000096, g-000575, g-000370, g-000337, g-000319, g-000364, g-000308, g-000293, g-000147, g-000307
g-000038, g-000492, g-000541, g-000185, g-000008, g-000482, g-000562, g-000097, g-000222, g-000084
g-000141, g-000377, g-000224, g-000223, g-000136, g-000434, g-000277, g-000426, g-000139, g-000093
PC_ 4
Positive: g-000006, g-000043, g-000462, g-000279, g-000180, g-000576, g-000087, g-000584, g-000498, g-000333
g-000189, g-000088, g-000451, g-000059, g-000135, g-000281, g-000106, g-000429, g-000316, g-000578
g-000303, g-000031, g-000581, g-000026, g-000122, g-000561, g-000546, g-000164, g-000353, g-000300
Negative: g-000072, g-000012, g-000129, g-000052, g-000097, g-000262, g-000080, g-000056, g-000025, g-000092
g-000354, g-000334, g-000423, g-000228, g-000002, g-000010, g-000086, g-000147, g-000185, g-000172
g-000124, g-000009, g-000077, g-000476, g-000126, g-000145, g-000065, g-000268, g-000152, g-000348
PC_ 5
Positive: g-000051, g-000150, g-000088, g-000476, g-000344, g-000116, g-000428, g-000012, g-000523, g-000394
g-000101, g-000127, g-000069, g-000214, g-000049, g-000357, g-000075, g-000081, g-000576, g-000342
g-000439, g-000018, g-000070, g-000079, g-000015, g-000550, g-000600, g-000247, g-000218, g-000331
Negative: g-000105, g-000037, g-000110, g-000054, g-000090, g-000389, g-000022, g-000578, g-000289, g-000147
g-000547, g-000011, g-000477, g-000433, g-000200, g-000348, g-000404, g-000003, g-000250, g-000109
g-000402, g-000241, g-000595, g-000341, g-000560, g-000385, g-000413, g-000352, g-000573, g-000265
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1000
Number of edges: 67836
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5999
Number of communities: 2
Elapsed time: 0 seconds
Clusterizations found: RNA_snn_res.0.8, seurat_clusters
Conditions found: orig.ident
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.872191190719604
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.03167200088501
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.94365358352661
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.882846117019653
Dataset analysis elapsed time: 4.69869089126587
COTAN dataset analysis: DONE
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.859636783599854
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.04784870147705
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.94465017318726
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.88124203681946
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0133342742919922
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.069279670715332
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.915916204452515
Total calculations elapsed time: 3.8797721862793
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.81443643569946
Dataset analysis elapsed time: 8.61872339248657
COTAN dataset analysis: 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
Total calculations elapsed time: 0.00707030296325684
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
Total calculations elapsed time: 0.0112769603729248
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 6
Number of rows (U set): 60
Total calculations elapsed time: 0.948342800140381
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
Total calculations elapsed time: 0.00867128372192383
calculating PValues: DONE
Number of selected secondary markers: 98
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00992488861083984
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 98
Number of rows (U set): 60
Total calculations elapsed time: 0.95385479927063
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
Total calculations elapsed time: 0.00889253616333008
calculating PValues: DONE
Number of selected secondary markers: 98
Calculating S: START
Calculating S: DONE
Calculate `GDI`: START
Effective number of cores used: 1
Executing 1 genes batches
Total calculations elapsed time: 0.00957322120666504
Calculate `GDI`: DONE
Number of columns (V set - secondary markers): 98
Number of rows (U set): 60
Total calculations elapsed time: 0.919764995574951
Calculating gene co-expression space - DONE
Total calculations elapsed time: 1.01462507247925
Establishing gene clusters - DONE
Initializing `COTAN` meta-data
COTAN dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.902066469192505
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.01182436943054
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.91761016845703
COTAN genes' COEX estimation not requested
Only genes' COEX elapsed time: 0.878229141235352
Dataset analysis elapsed time: 4.69790577888489
COTAN dataset analysis: DONE
Differential Expression Analysis - START
* DEA on cluster '1' with 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 313 cells
* DEA on cluster '4' with 188 cells
Total calculations elapsed time: 0.048694372177124
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'
Total calculations elapsed time: 3.56869554519653
Log Fold Change Analysis - DONE
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.10997640736885
Handling cluster '2' with mean UDE 1.00770245700749
Handling cluster '3' with mean UDE 0.95940682189354
Handling cluster '4' with mean UDE 0.907328369455933
clustersDeltaExpression - DONE
In group G1 there are 3 detected over 3 genes
In group G2 there are 2 detected over 3 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 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 313 cells
* DEA on cluster '4' with 188 cells
Total calculations elapsed time: 0.0523681640625
Differential Expression Analysis - DONE
Updating check results for the 0 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("1", "2")
*1_2-merge
Asked to drop 0 genes and 501 cells
COTAN dataset analysis: START
Asked to drop 16 genes and 0 cells
Genes/cells selection done: dropped [16] genes and [0] cells
Working on [584] genes and [499] cells
Dataset cleaning elapsed time: 0.931533575057983
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 10 iterations
Total calculations elapsed time: 1.92659902572632
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644
Model parameter estimation elapsed time: 2.81081390380859
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.81806302070618
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0142321586608887
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0403633117675781
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.928609132766724
Total calculations elapsed time: 3.80126762390137
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.6851978302002
Dataset analysis elapsed time: 8.42754530906677
COTAN dataset analysis: DONE
Checking uniformity for the cluster '1_2-merge' with 499 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
Total calculations elapsed time: 0.0340063571929932
Calculate `GDI`: DONE
Total calculations elapsed time: 2.76229023933411
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0538864135742188
Clean plots: DONE
GDI plot
Removed 1 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge, with size 499, is not uniform
Cluster 1_2-merge's shift to uniformity: 0.0566581136434268
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.178082191780822, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.35365811364343, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.148972602739726, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.37149326865969, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.00513698630136986, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.38256306292787, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 3, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.42111642638122, isUniform = FALSE, clusterSize = 499
Clusters 1 and 2 cannot be merged
Finished the first batch - no merges were executed
Loop calculations elapsed time: 16.2649829387665
Start merging nearest clusters: iteration 2
Differential Expression Analysis - START
* DEA on cluster '1' with 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 313 cells
* DEA on cluster '4' with 188 cells
Total calculations elapsed time: 0.0481462478637695
Differential Expression Analysis - DONE
Updating check results for the 1 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("3", "4")
*3_4-merge
Asked to drop 0 genes and 499 cells
COTAN dataset analysis: START
Asked to drop 37 genes and 0 cells
Genes/cells selection done: dropped [37] genes and [0] cells
Working on [563] genes and [501] cells
Dataset cleaning elapsed time: 0.968459844589233
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 11 iterations
Total calculations elapsed time: 1.96056723594666
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.107568326617881 | max: 698.639334552754 | % negative: 32.1492007104796
Model parameter estimation elapsed time: 2.89974308013916
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.78953051567078
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.012096643447876
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0381395816802979
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.903315544128418
Total calculations elapsed time: 3.74308228492737
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.65588736534119
Dataset analysis elapsed time: 8.52409029006958
COTAN dataset analysis: DONE
Checking uniformity for the cluster '3_4-merge' with 501 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
Total calculations elapsed time: 0.0307347774505615
Calculate `GDI`: DONE
Total calculations elapsed time: 2.64032673835754
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0524046421051025
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 3_4-merge, with size 501, is not uniform
Cluster 3_4-merge's shift to uniformity: 0.0813107504723543
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.297, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.259325044404973, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 1.37831075047235, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.307, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.216696269982238, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 1.41473792188167, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.4, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.0301953818827709, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 1.43341610223243, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.4, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 17, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 1.46173948790285, isUniform = FALSE, clusterSize = 501
Clusters 3 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 2 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 257 cells
* DEA on cluster '2' with 242 cells
* DEA on cluster '3' with 313 cells
* DEA on cluster '4' with 188 cells
Total calculations elapsed time: 0.044450044631958
Differential Expression Analysis - DONE
Updating check results for the 2 already tested pairs to align to new checker
1 new clusters pairs to be tested for merging:
c("2", "4")
*2_4-merge
Asked to drop 0 genes and 570 cells
COTAN dataset analysis: START
Asked to drop 9 genes and 0 cells
Genes/cells selection done: dropped [9] genes and [0] cells
Working on [591] genes and [430] cells
Dataset cleaning elapsed time: 0.890166759490967
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 1.89157390594482
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0739592351622374 | max: 400.051960722894 | % negative: 25.7191201353638
Model parameter estimation elapsed time: 2.76053190231323
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.76242089271545
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0138506889343262
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0390112400054932
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.871243238449097
Total calculations elapsed time: 3.68652606010437
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.57881116867065
Dataset analysis elapsed time: 8.22950983047485
COTAN dataset analysis: DONE
Checking uniformity for the cluster '2_4-merge' with 430 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
Total calculations elapsed time: 0.0318582057952881
Calculate `GDI`: DONE
Total calculations elapsed time: 2.72864937782288
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0524890422821045
Clean plots: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 2_4-merge, with size 430, is not uniform
Cluster 2_4-merge's shift to uniformity: 3.07228472969514
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.583756345177665, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 3.7954982715656, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.576988155668359, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 4.08354952912925, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.524534686971235, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 4.42722016730736, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 310, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 4.57228472969514, isUniform = FALSE, clusterSize = 430
Clusters 2 and 4 cannot be merged
Clusters 1 and 2 will be merged
Clusters 4 and 3 will be merged
Executed 2 merges
Loop calculations elapsed time: 15.9370024204254
Start merging nearest clusters: iteration 4
Differential Expression Analysis - START
* DEA on cluster '1_2-merge' with 499 cells
* DEA on cluster '3_4-merge' with 501 cells
Total calculations elapsed time: 0.0444159507751465
Differential Expression Analysis - DONE
Updating check results for the 3 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 dataset analysis: START
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1000] cells
Dataset cleaning elapsed time: 0.905847072601318
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 7 iterations
Total calculations elapsed time: 2.04473519325256
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0529252975916502 | max: 462.908586418992 | % negative: 17.3333333333333
Model parameter estimation elapsed time: 2.94910597801208
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.86283469200134
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0132994651794434
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0642876625061035
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.880604982376099
Total calculations elapsed time: 3.82102680206299
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.71870040893555
Dataset analysis elapsed time: 8.57365345954895
COTAN dataset analysis: DONE
Checking uniformity for the cluster '1_2-merge_3_4-merge-merge' with 1000 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
Total calculations elapsed time: 0.0321419239044189
Calculate `GDI`: DONE
Total calculations elapsed time: 2.6218090057373
Calculate GDI dataframe: DONE
Clean plots: START
Total calculations elapsed time: 0.0525896549224854
Clean plots: 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 1000, is not uniform
Cluster 1_2-merge_3_4-merge-merge's shift to uniformity: 3.8698838512041
class = AdvancedGDIUniformityCheck, firstCheck.isCheckAbove = FALSE, firstCheck.GDIThreshold = 1.397, firstCheck.maxRatioBeyond = 0.05, firstCheck.maxRankBeyond = 0, firstCheck.fractionBeyond = 0.69, firstCheck.thresholdRank = 0, firstCheck.quantileAtRatio = 4.54596809454194, firstCheck.quantileAtRank = NaN, secondCheck.isCheckAbove = TRUE, secondCheck.GDIThreshold = 1.407, secondCheck.maxRatioBeyond = 0.02, secondCheck.maxRankBeyond = 0, secondCheck.fractionBeyond = 0.678333333333333, secondCheck.thresholdRank = 0, secondCheck.quantileAtRatio = 4.93144728766684, secondCheck.quantileAtRank = NaN, thirdCheck.isCheckAbove = FALSE, thirdCheck.GDIThreshold = 1.5, thirdCheck.maxRatioBeyond = 0.01, thirdCheck.maxRankBeyond = 0, thirdCheck.fractionBeyond = 0.593333333333333, thirdCheck.thresholdRank = 0, thirdCheck.quantileAtRatio = 5.25322968524779, thirdCheck.quantileAtRank = NaN, fourthCheck.isCheckAbove = FALSE, fourthCheck.GDIThreshold = 1.5, fourthCheck.maxRatioBeyond = NaN, fourthCheck.maxRankBeyond = 2, fourthCheck.fractionBeyond = NaN, fourthCheck.thresholdRank = 356, fourthCheck.quantileAtRatio = NaN, fourthCheck.quantileAtRank = 5.3698838512041, isUniform = FALSE, clusterSize = 1000
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 4 checks
The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge
Differential Expression Analysis - START
* DEA on cluster '1' with 499 cells
* DEA on cluster '2' with 501 cells
Total calculations elapsed time: 0.0407710075378418
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Total calculations elapsed time: 64.6234772205353
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'
Total calculations elapsed time: 1.80093717575073
Log Fold Change Analysis - DONE
[1] "Tested cluster: 1"
Asked to drop 0 genes and 501 cells
COTAN dataset analysis: START
Asked to drop 16 genes and 0 cells
Genes/cells selection done: dropped [16] genes and [0] cells
Working on [584] genes and [499] cells
Dataset cleaning elapsed time: 0.889388799667358
Estimate `dispersion`: START
Effective number of cores used: 1
Executing 1 genes batches
Parallel dispersion Newton-Raphson: used up to 10 iterations
Total calculations elapsed time: 1.84168767929077
Estimate `dispersion`: DONE
Estimate `dispersion`: DONE
`dispersion` | min: -0.0608154544840047 | max: 1260.06995351592 | % negative: 35.6164383561644
Model parameter estimation elapsed time: 2.7586944103241
COTAN genes' COEX estimation: START
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 available yet
Calculate genes' COEX (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.75918745994568
Calculating genes' COEX normalization factor
Calculate genes' normalization factor elapsed time: 0.0126006603240967
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0379211902618408
Estimating genes' COEX
Calculate genes' COEX elapsed time: 0.84223461151123
Total calculations elapsed time: 3.65194392204285
Calculate genes' COEX (legacy): DONE
Only genes' COEX elapsed time: 4.52060103416443
Dataset analysis elapsed time: 8.16868424415588
COTAN dataset analysis: 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
Total calculations elapsed time: 0.0325396060943604
Calculate `GDI`: DONE
Total calculations elapsed time: 2.59963655471802
Calculate GDI dataframe: DONE
Dispersion bisection: straddling used 2 iterations
Dispersion bisection: used 8 iterations
Dispersion bisection: straddling used 1 iterations
Dispersion bisection: used 9 iterations
Dispersion Newton-Raphson: used up to 4 iterations
Dispersion Newton-Raphson: used up to 4 iterations
parallel dispersion bisection: straddling used up to 2 iterations
Parallel dispersion bisection: used up to 9 iterations
Parallel dispersion Newton-Raphson: used up to 4 iterations
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 572 ]
[ FAIL 0 | WARN 3 | SKIP 0 | PASS 572 ]
>
> proc.time()
user system elapsed
660.279 4.935 665.315
COTAN.Rcheck/COTAN-Ex.timings
| name | user | system | elapsed | |
| COTAN_Legacy | 0.002 | 0.000 | 0.003 | |
| COTAN_ObjectCreation | 9.080 | 0.185 | 9.126 | |
| CalculatingCOEX | 48.561 | 0.287 | 48.377 | |
| ClustersList | 0.012 | 0.000 | 0.011 | |
| Conversions | 4.576 | 0.016 | 4.602 | |
| GenesStatistics | 9.981 | 0.028 | 9.871 | |
| HandleMetaData | 0.046 | 0.000 | 0.046 | |
| HandlingClusterizations | 42.943 | 0.167 | 43.072 | |
| HandlingConditions | 0.095 | 0.000 | 0.096 | |
| HeatmapPlots | 31.326 | 0.288 | 31.294 | |
| Installing_torch | 0.000 | 0.000 | 0.001 | |
| LoggingFunctions | 0.002 | 0.000 | 0.003 | |
| ParametersEstimations | 21.272 | 0.175 | 21.502 | |
| RawDataCleaning | 5.353 | 0.008 | 5.378 | |
| RawDataGetters | 0.047 | 0.000 | 0.047 | |
| UniformClusters | 62.391 | 0.210 | 62.427 | |
| getColorsVector | 0.001 | 0.000 | 0.001 | |