Galfrè Silvia Giulia
| Snapshot Date: 2024-06-19 14:00 -0400 (Wed, 19 Jun 2024) |
| git_url: https://git.bioconductor.org/packages/COTAN |
| git_branch: RELEASE_3_19 |
| git_last_commit: 25fcc0b |
| git_last_commit_date: 2024-06-09 11:20:03 -0400 (Sun, 09 Jun 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-21 17:38 -0400 (Fri, 21 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4758 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4492 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4506 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4464 |
| 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 449/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| COTAN 2.4.3 (landing page) Galfrè Silvia Giulia
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the COTAN package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/COTAN.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: COTAN |
| Version: 2.4.3 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings COTAN_2.4.3.tar.gz |
| StartedAt: 2024-06-19 22:00:08 -0400 (Wed, 19 Jun 2024) |
| EndedAt: 2024-06-19 22:24:49 -0400 (Wed, 19 Jun 2024) |
| EllapsedTime: 1481.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: COTAN.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:COTAN.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings COTAN_2.4.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/COTAN.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘COTAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COTAN’ version ‘2.4.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘COTAN’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘torch’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘ggplot2:::ggname’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GDIPlot: no visible binding for global variable ‘sum.raw.norm’
GDIPlot: no visible binding for global variable ‘GDI’
UMAPPlot: no visible binding for global variable ‘x’
UMAPPlot: no visible binding for global variable ‘y’
calculateCoex_Legacy: no visible binding for global variable
‘expectedNN’
calculateCoex_Legacy: no visible binding for global variable
‘expectedNY’
calculateCoex_Legacy: no visible binding for global variable
‘expectedYN’
calculateCoex_Legacy: no visible binding for global variable
‘expectedYY’
calculateCoex_Legacy: no visible binding for global variable
‘observedYY’
calculateCoex_Legacy: no visible binding for global variable ‘.’
calculateG: no visible binding for global variable ‘observedNN’
calculateG: no visible binding for global variable ‘observedNY’
calculateG: no visible binding for global variable ‘observedYN’
calculateG: no visible binding for global variable ‘observedYY’
calculateG: no visible binding for global variable ‘expectedNN’
calculateG: no visible binding for global variable ‘expectedNY’
calculateG: no visible binding for global variable ‘expectedYN’
calculateG: no visible binding for global variable ‘expectedYY’
calculatePartialCoex: no visible binding for global variable
‘expectedNN’
calculatePartialCoex: no visible binding for global variable
‘expectedNY’
calculatePartialCoex: no visible binding for global variable
‘expectedYN’
calculatePartialCoex: no visible binding for global variable
‘expectedYY’
calculatePartialCoex: no visible binding for global variable
‘observedYY’
calculatePartialCoex: no visible binding for global variable ‘.’
cellsUniformClustering: no visible binding for global variable
‘objSeurat’
cellsUniformClustering: no visible binding for global variable
‘usedMaxResolution’
cellsUniformClustering: no visible binding for global variable
‘permMap’
checkClusterUniformity: ... may be used in an incorrect context:
‘c(..., nuPlot, zoomedNuPlot)’
checkClusterUniformity: no visible binding for global variable ‘nuPlot’
checkClusterUniformity: no visible binding for global variable
‘zoomedNuPlot’
cleanPlots: no visible binding for global variable ‘PC1’
cleanPlots: no visible binding for global variable ‘PC2’
cleanPlots: no visible binding for global variable ‘n’
cleanPlots: no visible binding for global variable ‘means’
cleanPlots: no visible binding for global variable ‘nu’
clustersMarkersHeatmapPlot: no visible binding for global variable
‘condName’
clustersMarkersHeatmapPlot: no visible binding for global variable
‘conditions’
clustersSummaryPlot: no visible binding for global variable ‘keys’
clustersSummaryPlot: no visible binding for global variable ‘values’
clustersSummaryPlot: no visible binding for global variable
‘CellNumber’
clustersSummaryPlot: no visible binding for global variable ‘ExpGenes’
clustersSummaryPlot: no visible binding for global variable ‘Cluster’
clustersSummaryPlot: no visible binding for global variable ‘Condition’
establishGenesClusters: no visible binding for global variable
‘secondaryMarkers’
establishGenesClusters: no visible binding for global variable ‘GCS’
establishGenesClusters: no visible binding for global variable
‘rankGenes’
expectedContingencyTables: no visible binding for global variable
‘expectedN’
expectedPartialContingencyTables: no visible binding for global
variable ‘expectedNN’
expectedPartialContingencyTables: no visible binding for global
variable ‘expectedN’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘group’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘y’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘x’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘width’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘violinwidth’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘xmax’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘xminv’
geom_flat_violin : <anonymous>: no visible binding for global variable
‘xmaxv’
heatmapPlot: no visible binding for global variable ‘g2’
mergeUniformCellsClusters : testPairListMerge: no visible binding for
global variable ‘cl1’
mergeUniformCellsClusters : testPairListMerge: no visible binding for
global variable ‘cl2’
mergeUniformCellsClusters: no visible binding for global variable
‘permMap’
mitochondrialPercentagePlot: no visible binding for global variable
‘mit.percentage’
observedContingencyTables: no visible binding for global variable
‘observedY’
observedPartialContingencyTables: no visible binding for global
variable ‘observedYY’
observedPartialContingencyTables: no visible binding for global
variable ‘observedY’
scatterPlot: no visible binding for global variable ‘.x’
calculateCoex,COTAN: no visible binding for global variable ‘useTorch’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘rawNorm’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘nu’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘lambda’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘a’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘hk’
coerce,COTAN-scCOTAN: no visible binding for global variable ‘clusters’
coerce,COTAN-scCOTAN: no visible binding for global variable
‘clusterData’
Undefined global functions or variables:
. .x CellNumber Cluster Condition ExpGenes GCS GDI PC1 PC2 a cl1 cl2
clusterData clusters condName conditions expectedN expectedNN
expectedNY expectedYN expectedYY g2 group hk keys lambda means
mit.percentage n nu nuPlot objSeurat observedNN observedNY observedY
observedYN observedYY permMap rankGenes rawNorm secondaryMarkers
sum.raw.norm useTorch usedMaxResolution values violinwidth width x
xmax xmaxv xminv y zoomedNuPlot
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
UniformClusters 132.319 0.562 131.076
CalculatingCOEX 45.899 0.778 45.311
HeatmapPlots 38.588 0.659 38.246
ParametersEstimations 21.839 0.240 22.061
HandlingClusterizations 18.006 0.235 18.148
GenesStatistics 8.682 0.232 8.472
COTANObjectCreation 7.803 0.251 7.742
RawDataCleaning 6.339 0.136 6.398
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.19-bioc/meat/COTAN.Rcheck/00check.log’
for details.
COTAN.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL COTAN ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘COTAN’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading Note: ... may be used in an incorrect context ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (COTAN)
COTAN.Rcheck/tests/outputTestDatasetCreation.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
> # Creates the files to be reloaded by the tests for comparisons
> library(zeallot)
>
> outputTestDatasetCreation <- function(testsDir = file.path("tests",
+ "testthat")) {
+ utils::data("test.dataset", package = "COTAN")
+ options(parallelly.fork.enable = TRUE)
+
+ obj <- COTAN(raw = test.dataset)
+ obj <- initializeMetaDataset(obj, GEO = " ",
+ sequencingMethod = "artificial",
+ sampleCondition = "test")
+
+ obj <- proceedToCoex(obj, cores = 6L, saveObj = FALSE)
+ #saveRDS(obj, file = file.path(testsDir,"temp.RDS"))
+
+ cells.names.test <- getCells(obj)[c(1L:10L, 591L:610L, 991L:1000L)]
+ genes.names.test <- getGenes(obj)[c(1L:10L, 291L:310L, 591L: 600L)]
+ saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS"))
+ saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS"))
+
+ dispersion.test <- getDispersion(obj)[genes.names.test]
+ saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS"))
+
+ raw.norm.test <- getNormalizedData(obj)[genes.names.test, cells.names.test]
+ saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS"))
+
+ coex.test <- getGenesCoex(obj, genes = genes.names.test, zeroDiagonal = FALSE)
+ saveRDS(coex.test, file.path(testsDir, "coex.test.RDS"))
+
+ lambda.test <- getLambda(obj)[genes.names.test]
+ saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS"))
+
+ GDI.test <- calculateGDI(obj)
+ GDI.test <- GDI.test[genes.names.test, ]
+ saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS"))
+
+ nu.test <- getNu(obj)[cells.names.test]
+ saveRDS(nu.test, file.path(testsDir, "nu.test.RDS"))
+
+ pval.test <- calculatePValue(obj, geneSubsetCol = genes.names.test)
+ saveRDS(pval.test, file.path(testsDir, "pval.test.RDS"))
+
+ GDIThreshold <- 1.46
+ initialResolution <- 0.8
+
+ clusters <- cellsUniformClustering(obj, GDIThreshold = GDIThreshold,
+ initialResolution = initialResolution,
+ cores = 6L, saveObj = FALSE)[["clusters"]]
+ saveRDS(clusters, file.path(testsDir, "clusters1.RDS"))
+
+ coexDF <- DEAOnClusters(obj, clusters = clusters)
+ obj <- addClusterization(obj, clName = "clusters",
+ clusters = clusters, coexDF = coexDF)
+
+ saveRDS(coexDF[genes.names.test, ],
+ file.path(testsDir, "coex.test.cluster1.RDS"))
+
+ pvalDF <- pValueFromDEA(coexDF, getNumCells(obj), method = "none")
+
+ saveRDS(pvalDF[genes.names.test, ],
+ file.path(testsDir, "pval.test.cluster1.RDS"))
+
+ c(mergedClusters, mCoexDF) %<-%
+ mergeUniformCellsClusters(objCOTAN = obj,
+ clusters = NULL,
+ GDIThreshold = GDIThreshold,
+ cores = 6L,
+ distance = "cosine",
+ hclustMethod = "ward.D2",
+ saveObj = FALSE)
+
+ saveRDS(mergedClusters[genes.names.test],
+ file.path(testsDir, "cluster_data_merged.RDS"))
+ }
>
> proc.time()
user system elapsed
0.176 0.030 0.193
COTAN.Rcheck/tests/spelling.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> if (requireNamespace('spelling', quietly = TRUE))
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+ skip_on_cran = TRUE)
NULL
>
> proc.time()
user system elapsed
0.164 0.036 0.189
COTAN.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> Sys.setenv(R_TESTS = "")
> library(testthat)
> library(COTAN)
> test_check("COTAN")
Setting new log level to 4
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.35892510414124
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00129485130310059
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00689077377319336
Estimating genes' coex
Calculate genes' coex elapsed time: 0.763200283050537
Total calculations elapsed time: 3.13031101226807
Calculate genes' coex (legacy): DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 4 genes batches from [1:2] to [7:8]
Executing 1 genes batches from [9:10] to [9:10]
Estimate dispersion: DONE
dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:3] to [10:11]
Executing 3 cells batches from [12:14] to [18:20]
Estimate nu: DONE
nu change (abs) | max: 1.75595238095238 | median: 1.07174634176587 | mean: 1.07174634176587
Estimate 'dispersion'/'nu': START
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 1.0362548828125 | max: 4.60986328125 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.0265938895089288 | median: 0.0144680038331048 | mean: 0.0144680038331048
Nu mean: 1.69633192486233
Marginal errors | max: 1.95570586131367 | median 1.32068160171502 | mean: 1.33375826507259
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.058837890625 | max: 3.528076171875 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.416683423613994 | median: 0.239880630367975 | mean: 0.239880630367975
Nu mean: 0.823197206753982
Marginal errors | max: 0.836359531101206 | median 0.703684202571891 | mean: 0.645537958989614
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.32879638671875 | max: 4.0302734375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.164237872898673 | median: 0.0955985184389135 | mean: 0.0955985184389135
Nu mean: 1.06863935445976
Marginal errors | max: 0.259872988828242 | median 0.213703042752633 | mean: 0.197386407582083
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2294921875 | max: 3.8720703125 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.055185575120883 | median: 0.0319991762044448 | mean: 0.0319991762044448
Nu mean: 0.976813601083562
Marginal errors | max: 0.0951586919577032 | median 0.079429703709466 | mean: 0.0724140148396648
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2637939453125 | max: 3.929443359375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.0196211148938294 | median: 0.01138609597457 | mean: 0.01138609597457
Nu mean: 1.00823501891926
Marginal errors | max: 0.0327747321002292 | median 0.0272104747849538 | mean: 0.0248963830312038
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.25177001953125 | max: 3.90966796875 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.00670099066960717 | median: 0.00388888266671264 | mean: 0.00388888266671264
Nu mean: 0.997187891997105
Marginal errors | max: 0.0114324509186883 | median 0.0094232649770607 | mean: 0.00863113610779571
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.25592041015625 | max: 3.91650390625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.00230093811689414 | median: 0.00132529122122246 | mean: 0.00132529122122246
Nu mean: 1.00097564689567
Marginal errors | max: 0.00387133150664631 | median 0.0031091017608853 | mean: 0.00286071175800213
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2545166015625 | max: 3.914306640625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.000837011646904529 | median: 0.000470837393363011 | mean: 0.000470837393363011
Nu mean: 0.999633825746458
Marginal errors | max: 0.00122501723202006 | median 0.00102126435760308 | mean: 0.000943992659051318
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.000209227351122054 | median: 0.000122070312500028 | mean: 0.000122070312500028
Nu mean: 1.00008715703862
Marginal errors | max: 0.000364602956581805 | median 0.000313956936819793 | mean: 0.000282899574318485
Estimate dispersion/nu: DONE
Estimate 'dispersion'/'nu': START
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.45722818374634
Calculating genes' coex normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.000758647918701172
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00306129455566406
Estimating genes' coex
Calculate genes' coex elapsed time: 0.877479553222656
Total calculations elapsed time: 3.33852767944336
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: 2.50721549987793
Calculating cells' coex normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000772953033447266
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00243043899536133
Estimating cells' coex
Calculate cells' coex elapsed time: 0.868036985397339
Total calculations elapsed time: 3.37845587730408
Calculate cells' coex (legacy): DONE
Initializing `COTAN` meta-data
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate 'dispersion'/'nu': START
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014
Nu mean: 1.68489292689732
Marginal errors | max: 1.73564890252257 | median 1.37996360874076 | mean: 1.32180348113228
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.0655517578125 | max: 3.5439453125 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.402649984216273 | median: 0.231868788425666 | mean: 0.231868788425666
Nu mean: 0.829218804209393
Marginal errors | max: 0.80321315986594 | median 0.677497553540581 | mean: 0.619375430892821
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.3260498046875 | max: 4.026123046875 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.158004893526231 | median: 0.0919692884670312 | mean: 0.0919692884670312
Nu mean: 1.0660356050592
Marginal errors | max: 0.250724014302326 | median 0.206232152124436 | mean: 0.190425623677198
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.23040771484375 | max: 3.8736572265625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.0532774732102337 | median: 0.0308837890624999 | mean: 0.0308837890624999
Nu mean: 0.977606315852266
Marginal errors | max: 0.0916983669060123 | median 0.0765266929824948 | mean: 0.0697593208689684
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.26348876953125 | max: 3.928955078125 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.0189966206463044 | median: 0.0110199320575908 | mean: 0.0110199320575908
Nu mean: 1.00797668858871
Marginal errors | max: 0.0317151207459254 | median 0.0262702142278251 | mean: 0.0240886952086962
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2518310546875 | max: 3.9097900390625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.00670088501353994 | median: 0.00388888101583662 | mean: 0.00388888101583662
Nu mean: 0.997187996002297
Marginal errors | max: 0.0113693316356223 | median 0.00939669372836249 | mean: 0.00860715734056932
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2559814453125 | max: 3.9166259765625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.00251007446998996 | median: 0.00144735987374958 | mean: 0.00144735987374958
Nu mean: 1.00106271459624
Marginal errors | max: 0.00406746973787442 | median 0.00343393462175534 | mean: 0.00313496757119527
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.25445556640625 | max: 3.9140625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.000837027590858019 | median: 0.000488281249999889 | mean: 0.000488281249999889
Nu mean: 0.999651253659142
Marginal errors | max: 0.00143433714371533 | median 0.00116636244706747 | mean: 0.00109289166947839
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:10] to [1:10]
Estimate dispersion: DONE
dispersion | min: 0.2550048828125 | max: 3.9150390625 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 1 cells batches from [1:20] to [1:20]
Estimate nu: DONE
nu change (abs) | max: 0.000209227688885871 | median: 0.0001220703125 | mean: 0.0001220703125
Nu mean: 1.00008715737639
Marginal errors | max: 0.000379524846207957 | median 0.000325685250686547 | mean: 0.000295532844332236
Estimate dispersion/nu: DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.31283235549927
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.000584125518798828
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0014948844909668
Estimating genes' coex
Calculate genes' coex elapsed time: 0.749678134918213
Total calculations elapsed time: 3.06458950042725
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: 2.18971347808838
Calculating cells' coex normalization factor
Calculate cells' normalization factor elapsed time: 0.000661134719848633
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00169873237609863
Estimating cells' coex
Calculate cells' coex elapsed time: 0.704149007797241
Total calculations elapsed time: 2.89622235298157
Calculate cells' coex (legacy): DONE
Calculate genes' partial coex: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial coex normalization factor
Fraction of genes with very low expected contingency tables: 0.325
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial coex
Calculate genes' partial coex: DONE
Calculate cells' partial coex: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial coex normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial coex
Calculate cells' partial coex: DONE
Asked to drop 2 genes and 0 cells
Asked to drop 0 genes and 4 cells
Asked to drop 2 genes and 2 cells
Attaching package: 'rlang'
The following objects are masked from 'package:testthat':
is_false, is_null, is_true
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
calculating YY.. done
calculating YY.. done
calculating YN..NY..NN..t().. done
Estimate dispersion: START
Effective number of cores used: 1
Executing 3 genes batches from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 0.9033203125 | max: 4.6796875 | % negative: 10
calculating NN.. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.66926956176758
Calculating genes' coex normalization factor
Fraction of genes' with very low expected contingency tables: 0.181818181818182
Calculate genes' normalization factor elapsed time: 0.00092005729675293
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00190997123718262
Estimating genes' coex
Calculate genes' coex elapsed time: 0.918335437774658
Total calculations elapsed time: 3.59043502807617
Calculate genes' coex (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.35626029968262
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.000615835189819336
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00158524513244629
Estimating genes' coex
Calculate genes' coex elapsed time: 0.908047199249268
Total calculations elapsed time: 3.26650857925415
Calculate genes' coex (legacy): DONE
Calculate genes' partial coex: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial coex normalization factor
Fraction of genes with very low expected contingency tables: 0.1
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial coex
Calculate genes' partial coex: DONE
Calculate genes' partial coex: START
Retrieving expected genes' partial contingency table
calculating partial NN.. done
calculating partial NY..YN..YY.. done
Calculating genes' partial coex normalization factor
Fraction of genes with very low expected contingency tables: 0.4
Retrieving observed genes' yes/yes partial contingency table
calculating partial YY.. done
Estimating genes' partial coex
Calculate genes' partial coex: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
calculating YY.. done
calculating YY.. done
calculating NY..YN..NN..t().. done
Estimate 'dispersion'/'nu': START
Estimate dispersion: START
Effective number of cores used: 1
Executing 3 genes batches from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
Estimate nu: DONE
nu change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014
Nu mean: 1.68489292689732
Marginal errors | max: 0.25535328937316 | median 0.0807577993228135 | mean: 0.101980750205762
Estimate dispersion: START
Effective number of cores used: 1
Executing 3 genes batches from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 1.037109375 | max: 4.6107177734375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
Estimate nu: DONE
nu change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011
Nu mean: 1.69735147626627
Marginal errors | max: 0.00326864580272002 | median 0.00111524657842743 | mean: 0.00131556083122533
Estimate dispersion: START
Effective number of cores used: 1
Executing 3 genes batches from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
Estimate nu: DONE
nu change (abs) | max: 0 | median: 0 | mean: 0
Nu mean: 1.69735147626627
Marginal errors | max: 7.56328383637594e-05 | median 1.72948087246994e-05 | mean: 2.99252342145451e-05
Estimate dispersion/nu: DONE
calculating NN.. done
calculating NN.. done
calculating YN..NY..YY..t().. done
Calculate cells' coex (legacy): START
Retrieving expected cells' contingency table
calculating NN.. done
calculating YN..NY..YY..t().. done
Expected cells' contingency table elapsed time: 2.31457424163818
Calculating cells' coex normalization factor
Fraction of cells' with very low expected contingency tables: 0
Calculate cells' normalization factor elapsed time: 0.000720977783203125
Retrieving observed cells' yes/yes contingency table
calculating YY.. done
Observed cells' contingency table elapsed time: 0.00153565406799316
Estimating cells' coex
Calculate cells' coex elapsed time: 0.995063543319702
Total calculations elapsed time: 3.31189441680908
Calculate cells' coex (legacy): DONE
Calculate cells' partial coex: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial coex normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial coex
Calculate cells' partial coex: DONE
Calculate cells' partial coex: START
Retrieving expected cells' partial contingency table
calculating partial NN.. done
calculating partial YN..NY..YY.. done
Calculating cells' partial coex normalization factor
Fraction of genes with very low expected contingency tables: 0
Retrieving observed cells' yes/yes partial contingency table
calculating partial YY.. done
Estimating cells' partial coex
Calculate cells' partial coex: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Estimate 'dispersion'/'nu': START
Estimate dispersion: START
Effective number of cores used: 1
Executing 3 genes batches from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 0.903564453125 | max: 4.679443359375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
Estimate nu: DONE
nu change (abs) | max: 1.75719246031746 | median: 1.07229953342014 | mean: 1.07229953342014
Nu mean: 1.68489292689732
Marginal errors | max: 0.25535328937316 | median 0.0807577993228135 | mean: 0.101980750205762
Estimate dispersion: START
Effective number of cores used: 1
Executing 3 genes batches from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 1.037109375 | max: 4.6107177734375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
Estimate nu: DONE
nu change (abs) | max: 0.0273438105507502 | median: 0.0148852611818011 | mean: 0.0148852611818011
Nu mean: 1.69735147626627
Marginal errors | max: 0.00326864580272002 | median 0.00111524657842743 | mean: 0.00131556083122533
Estimate dispersion: START
Effective number of cores used: 1
Executing 3 genes batches from [1:3] to [8:10]
Estimate dispersion: DONE
dispersion | min: 1.03887939453125 | max: 4.6097412109375 | % negative: 10
Estimate nu: START
Effective number of cores used: 1
Executing 4 cells batches from [1:4] to [13:16]
Executing 1 cells batches from [17:20] to [17:20]
Estimate nu: DONE
nu change (abs) | max: 0 | median: 0 | mean: 0
Nu mean: 1.69735147626627
Marginal errors | max: 7.56328383637594e-05 | median 1.72948087246994e-05 | mean: 2.99252342145451e-05
Estimate dispersion/nu: DONE
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.38719582557678
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.000569343566894531
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00145983695983887
Estimating genes' coex
Calculate genes' coex elapsed time: 0.764542579650879
Total calculations elapsed time: 3.15376758575439
Calculate genes' coex (legacy): DONE
Calculating S: START
Calculating S: DONE
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Calculating G: DONE
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values genome wide on columns and genome wide on rows
calculating PValues: DONE
Using G
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Calculating G: DONE
calculating PValues: START
Get p-values on a set of genes on columns and on a set of genes on rows
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
Calculate GDI dataframe: START
Using G
Calculating G: START
calculating YY.. done
calculating YN..NY..NN..t().. done
calculating NN.. done
calculating NY..YN..YY..t().. done
Estimating G
Calculating G: DONE
S matrix sorted
Calculate GDI dataframe: DONE
Calculating S: START
Calculating S: DONE
S matrix sorted
S matrix sorted
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 3.0547890663147
Cotan genes' coex estimation started
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.92410397529602
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00627303123474121
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0461628437042236
Estimating genes' coex
Calculate genes' coex elapsed time: 0.779008150100708
Total calculations elapsed time: 3.75554800033569
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.53536105155945
Total elapsed time: 8.33381795883179
Initializing `COTAN` meta-data
Condition test
n cells 1200
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 2.82861423492432
Cotan genes' coex estimation started
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.71062779426575
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00581264495849609
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0451045036315918
Estimating genes' coex
Calculate genes' coex elapsed time: 0.725563049316406
Total calculations elapsed time: 3.48710799217224
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.21953940391541
Total elapsed time: 7.97276043891907
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 2.96902346611023
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.00073194503784
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00786924362182617
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0476205348968506
Estimating genes' coex
Calculate genes' coex elapsed time: 0.822587251663208
Total calculations elapsed time: 3.87880897521973
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.59797096252441
Total elapsed time: 8.30315136909485
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Condition test
n cells 1200
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 3.12048053741455
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.87294387817383
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00530457496643066
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.044736385345459
Estimating genes' coex
Calculate genes' coex elapsed time: 0.770700931549072
Total calculations elapsed time: 3.69368577003479
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.44422245025635
Total elapsed time: 8.43843126296997
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
Initializing `COTAN` meta-data
Asked to drop 0 genes and 1160 cells
Cotan analysis functions started
Asked to drop 31 genes and 0 cells
Genes/cells selection done: dropped [31] genes and [0] cells
Working on [569] genes and [40] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:569] to [1:569]
Estimate dispersion: DONE
dispersion | min: -0.2119140625 | max: 85.5 | % negative: 62.2144112478032
Cotan genes' coex estimation not requested
Total elapsed time: 3.82269906997681
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: 2.34917426109314
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00561833381652832
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00615119934082031
Estimating genes' coex
Calculate genes' coex elapsed time: 0.751579999923706
Total calculations elapsed time: 3.11252379417419
Calculate genes' coex (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.36592864990234
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00611090660095215
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00649905204772949
Estimating genes' coex
Calculate genes' coex elapsed time: 0.818183898925781
Total calculations elapsed time: 3.19672250747681
Calculate genes' coex (legacy): DONE
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.31731295585632
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00577163696289062
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.00614213943481445
Estimating genes' coex
Calculate genes' coex elapsed time: 0.729524374008179
Total calculations elapsed time: 3.05875110626221
Calculate genes' coex (legacy): DONE
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
PCA: START
PCA: DONE
Hierarchical clustering: START
Hierarchical clustering: DONE
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 8.66722798347473
Saving elaborated data locally at: /tmp/RtmphoORfh/test.cotan.RDS
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Creating Seurat object: START
Normalizing layer: counts
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix
|
| | 0%
|
|======================================================================| 100%
PC_ 1
Positive: g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528
g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583
g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541
Negative: g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140
g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135
g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128
PC_ 2
Positive: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087
g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207
g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158
Negative: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539
g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538
g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570
PC_ 3
Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360
g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470
g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317
Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303
g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262
g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241
PC_ 4
Positive: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079
g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228
g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150
Negative: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131
g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366
g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306
PC_ 5
Positive: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237
g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505
g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393
Negative: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578
g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381
g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 55489
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
22:13:50 UMAP embedding parameters a = 0.9922 b = 1.112
22:13:50 Read 1200 rows and found 50 numeric columns
22:13:50 Using Annoy for neighbor search, n_neighbors = 30
22:13:50 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:13:50 Writing NN index file to temp file /tmp/RtmphoORfh/file1473a56bd26243
22:13:50 Searching Annoy index using 1 thread, search_k = 3000
22:13:51 Annoy recall = 100%
22:13:51 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:13:53 Initializing from normalized Laplacian + noise (using RSpectra)
22:13:53 Commencing optimization for 500 epochs, with 42274 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:13:55 Optimization finished
Creating PDF UMAP in file: /tmp/RtmphoORfh/test/reclustering/pdf_umap_1.pdf
Creating Seurat object: DONE
* checking uniformity of cluster '0' of 4 clusters
Asked to drop 0 genes and 847 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [353] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.038818359375 | max: 11.109375 | % negative: 5
Only analysis elapsed time: 2.68429803848267
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.77285218238831
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00825810432434082
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0376002788543701
Estimating genes' coex
Calculate genes' coex elapsed time: 0.813284873962402
Total calculations elapsed time: 3.63199543952942
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.35010766983032
Total elapsed time: 7.89779162406921
Checking uniformity for the cluster '01_0000' with 353 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0000, with size 353, is uniform
0.83% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.4439
cluster 01_0000 is uniform
* checking uniformity of cluster '1' of 4 clusters
Asked to drop 0 genes and 879 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [321] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5
Only analysis elapsed time: 2.50872325897217
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.70102667808533
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00622940063476562
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0312731266021729
Estimating genes' coex
Calculate genes' coex elapsed time: 0.835073232650757
Total calculations elapsed time: 3.57360243797302
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.4057023525238
Total elapsed time: 7.67354369163513
Checking uniformity for the cluster '01_0001' with 321 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 321, is uniform
0.5% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.4305
cluster 01_0001 is uniform
* checking uniformity of cluster '2' of 4 clusters
Asked to drop 0 genes and 905 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [295] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.054443359375 | max: 104 | % negative: 36.5
Only analysis elapsed time: 2.57706117630005
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.56705784797668
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00795364379882812
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0166709423065186
Estimating genes' coex
Calculate genes' coex elapsed time: 0.929856061935425
Total calculations elapsed time: 3.52153849601746
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.38675999641418
Total elapsed time: 7.87042737007141
Checking uniformity for the cluster '01_0002' with 295 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 295, is uniform
0% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.3925
cluster 01_0002 is uniform
* checking uniformity of cluster '3' of 4 clusters
Asked to drop 0 genes and 969 cells
Cotan analysis functions started
Asked to drop 1 genes and 0 cells
Genes/cells selection done: dropped [1] genes and [0] cells
Working on [599] genes and [231] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:599] to [1:599]
Estimate dispersion: DONE
dispersion | min: -0.0662841796875 | max: 82.5 | % negative: 33.889816360601
Only analysis elapsed time: 2.57801961898804
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.63049602508545
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00673341751098633
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.015777587890625
Estimating genes' coex
Calculate genes' coex elapsed time: 0.813867568969727
Total calculations elapsed time: 3.46687459945679
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.31104397773743
Total elapsed time: 7.74907803535461
Checking uniformity for the cluster '01_0003' with 231 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0003, with size 231, is uniform
0% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.373
cluster 01_0003 is uniform
Found 4 uniform and 0 non-uniform clusters
NO new possible uniform clusters! Unclustered cell left: 0
The final raw clusterization contains [ 4 ] different clusters: 01_0000, 01_0001, 01_0002, 01_0003
Differential Expression Analysis - START
* DEA on cluster '1'
* DEA on cluster '2'
* DEA on cluster '3'
* DEA on cluster '4'
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 3, 2 -> 1, 3 -> 2, 4 -> 4
Cluster, UMAP and Saving the Seurat dataset
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 55489
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.6846
Number of communities: 4
Elapsed time: 0 seconds
22:14:52 UMAP embedding parameters a = 0.9922 b = 1.112
22:14:52 Read 1200 rows and found 25 numeric columns
22:14:52 Using Annoy for neighbor search, n_neighbors = 30
22:14:52 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:14:52 Writing NN index file to temp file /tmp/RtmphoORfh/file1473a54c9c68f2
22:14:52 Searching Annoy index using 1 thread, search_k = 3000
22:14:53 Annoy recall = 100%
22:14:54 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:14:55 Initializing from normalized Laplacian + noise (using RSpectra)
22:14:55 Commencing optimization for 500 epochs, with 43428 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:14:58 Optimization finished
Creating cells' uniform clustering: DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2, 3 -> 3, 4 -> 4
Asked to drop 0 genes and 905 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [295] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.054443359375 | max: 104 | % negative: 36.5
Only analysis elapsed time: 2.60026454925537
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.88045763969421
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00854039192199707
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0164730548858643
Estimating genes' coex
Calculate genes' coex elapsed time: 0.816390752792358
Total calculations elapsed time: 3.72186183929443
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.6446795463562
Total elapsed time: 8.08143305778503
Checking uniformity for the cluster 'Cluster_2' with 295 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster Cluster_2, with size 295, is uniform
0% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.3925
Differential Expression Analysis - START
* DEA on cluster '-1'
* DEA on cluster '1'
* DEA on cluster '2'
* DEA on cluster '3'
* DEA on cluster '4'
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 2, 2 -> 1, 3 -> 4, 4 -> 3, -1 -> -1
Applied reordering to clusterization is:
1 -> 2, 2 -> 3, 3 -> 1, 4 -> 4, -1 -> -1
Creating cells' uniform clustering: START
In iteration 1 the number of cells to re-cluster is 1200 cells belonging to 0 clusters
Creating Seurat object: START
Normalizing layer: counts
Performing log-normalization
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Finding variable features for layer counts
Calculating gene variances
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Calculating feature variances of standardized and clipped values
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Centering and scaling data matrix
|
| | 0%
|
|======================================================================| 100%
PC_ 1
Positive: g-000558, g-000570, g-000499, g-000504, g-000546, g-000506, g-000503, g-000517, g-000596, g-000528
g-000527, g-000580, g-000592, g-000578, g-000509, g-000488, g-000555, g-000577, g-000534, g-000583
g-000598, g-000535, g-000512, g-000554, g-000519, g-000525, g-000548, g-000544, g-000502, g-000541
Negative: g-000133, g-000007, g-000074, g-000141, g-000057, g-000235, g-000170, g-000019, g-000195, g-000140
g-000183, g-000031, g-000046, g-000178, g-000177, g-000161, g-000157, g-000139, g-000011, g-000135
g-000125, g-000208, g-000061, g-000085, g-000204, g-000104, g-000237, g-000004, g-000038, g-000128
PC_ 2
Positive: g-000039, g-000050, g-000175, g-000078, g-000116, g-000189, g-000135, g-000047, g-000072, g-000087
g-000063, g-000235, g-000066, g-000109, g-000018, g-000074, g-000231, g-000136, g-000034, g-000207
g-000128, g-000167, g-000171, g-000049, g-000182, g-000013, g-000054, g-000062, g-000240, g-000158
Negative: g-000584, g-000583, g-000544, g-000519, g-000575, g-000516, g-000585, g-000486, g-000489, g-000539
g-000484, g-000502, g-000523, g-000595, g-000305, g-000574, g-000599, g-000589, g-000509, g-000538
g-000526, g-000551, g-000579, g-000590, g-000445, g-000556, g-000543, g-000501, g-000504, g-000570
PC_ 3
Positive: g-000015, g-000575, g-000483, g-000316, g-000025, g-000364, g-000050, g-000278, g-000443, g-000360
g-000332, g-000124, g-000212, g-000387, g-000536, g-000252, g-000251, g-000321, g-000501, g-000470
g-000582, g-000106, g-000455, g-000368, g-000081, g-000104, g-000437, g-000288, g-000386, g-000317
Negative: g-000211, g-000337, g-000129, g-000185, g-000397, g-000403, g-000253, g-000098, g-000390, g-000303
g-000052, g-000088, g-000463, g-000468, g-000236, g-000209, g-000005, g-000375, g-000342, g-000262
g-000388, g-000091, g-000413, g-000285, g-000003, g-000095, g-000142, g-000205, g-000432, g-000241
PC_ 4
Positive: g-000334, g-000398, g-000292, g-000095, g-000097, g-000202, g-000382, g-000195, g-000007, g-000079
g-000086, g-000240, g-000263, g-000317, g-000576, g-000557, g-000160, g-000154, g-000214, g-000228
g-000313, g-000053, g-000524, g-000374, g-000568, g-000188, g-000358, g-000528, g-000362, g-000150
Negative: g-000379, g-000193, g-000212, g-000434, g-000593, g-000513, g-000177, g-000223, g-000069, g-000131
g-000162, g-000345, g-000462, g-000484, g-000448, g-000229, g-000365, g-000302, g-000010, g-000366
g-000051, g-000535, g-000269, g-000270, g-000155, g-000529, g-000373, g-000008, g-000393, g-000306
PC_ 5
Positive: g-000451, g-000339, g-000295, g-000328, g-000544, g-000061, g-000227, g-000391, g-000556, g-000237
g-000067, g-000165, g-000449, g-000591, g-000087, g-000129, g-000197, g-000203, g-000487, g-000505
g-000333, g-000029, g-000271, g-000064, g-000583, g-000156, g-000448, g-000153, g-000526, g-000393
Negative: g-000518, g-000108, g-000186, g-000170, g-000401, g-000337, g-000047, g-000599, g-000432, g-000578
g-000042, g-000065, g-000493, g-000261, g-000533, g-000256, g-000560, g-000596, g-000368, g-000381
g-000535, g-000338, g-000215, g-000159, g-000365, g-000234, g-000173, g-000387, g-000225, g-000272
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 55489
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.5973
Number of communities: 4
Elapsed time: 0 seconds
Used resolution for Seurat clusterization is: 0.8
22:15:16 UMAP embedding parameters a = 0.9922 b = 1.112
22:15:16 Read 1200 rows and found 50 numeric columns
22:15:16 Using Annoy for neighbor search, n_neighbors = 30
22:15:16 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:15:16 Writing NN index file to temp file /tmp/RtmphoORfh/file1473a512d5a3fd
22:15:16 Searching Annoy index using 1 thread, search_k = 3000
22:15:16 Annoy recall = 100%
22:15:17 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:15:19 Initializing from normalized Laplacian + noise (using RSpectra)
22:15:19 Commencing optimization for 500 epochs, with 42274 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:15:22 Optimization finished
Creating PDF UMAP in file: /tmp/RtmphoORfh/test/reclustering/pdf_umap_1.pdf
Creating Seurat object: DONE
Using passed in clusterization
* checking uniformity of cluster '1' of 2 clusters
Asked to drop 0 genes and 600 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [600] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0386962890625 | max: 19.40625 | % negative: 6.5
Only analysis elapsed time: 3.05862760543823
Cotan genes' coex estimation started
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.14035820960999
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00580215454101562
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0351676940917969
Estimating genes' coex
Calculate genes' coex elapsed time: 0.834423542022705
Total calculations elapsed time: 4.0157516002655
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.97556734085083
Total elapsed time: 8.98737049102783
Checking uniformity for the cluster '01_0001' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0001, with size 600, is uniform
1% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.4534
cluster 01_0001 is uniform
* checking uniformity of cluster '2' of 2 clusters
Asked to drop 0 genes and 600 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [600] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.032958984375 | max: 10.0859375 | % negative: 3.66666666666667
Only analysis elapsed time: 2.893394947052
Cotan genes' coex estimation started
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 3.07759928703308
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00753045082092285
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0409419536590576
Estimating genes' coex
Calculate genes' coex elapsed time: 0.899793386459351
Total calculations elapsed time: 4.02586507797241
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.87385725975037
Total elapsed time: 8.60802698135376
Checking uniformity for the cluster '01_0002' with 600 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 01_0002, with size 600, is uniform
0.5% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.4378
cluster 01_0002 is uniform
Found 2 uniform and 0 non-uniform clusters
NO new possible uniform clusters! Unclustered cell left: 0
The final raw clusterization contains [ 2 ] different clusters: 01_0001, 01_0002
Differential Expression Analysis - START
* DEA on cluster '1'
* DEA on cluster '2'
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Cluster, UMAP and Saving the Seurat dataset
Computing nearest neighbor graph
Computing SNN
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
Number of nodes: 1200
Number of edges: 55489
Running Louvain algorithm with multilevel refinement...
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Maximum modularity in 10 random starts: 0.6846
Number of communities: 4
Elapsed time: 0 seconds
22:15:55 UMAP embedding parameters a = 0.9922 b = 1.112
22:15:55 Read 1200 rows and found 25 numeric columns
22:15:55 Using Annoy for neighbor search, n_neighbors = 30
22:15:55 Building Annoy index with metric = cosine, n_trees = 50
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:15:55 Writing NN index file to temp file /tmp/RtmphoORfh/file1473a5411995fd
22:15:55 Searching Annoy index using 1 thread, search_k = 3000
22:15:55 Annoy recall = 100%
22:15:56 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
22:15:58 Initializing from normalized Laplacian + noise (using RSpectra)
22:15:58 Commencing optimization for 500 epochs, with 43428 positive edges
Using method 'umap'
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
22:16:01 Optimization finished
Creating cells' uniform clustering: DONE
findClustersMarkers - START
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.20998115359079
Handling cluster '2' with mean UDE 0.538244816501366
Handling cluster '3' with mean UDE 1.43530796540674
Handling cluster '4' with mean UDE 0.632684489354434
clustersDeltaExpression - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'
Log Fold Change Analysis - DONE
findClustersMarkers - DONE
findClustersMarkers - START
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.20998115359079
Handling cluster '2' with mean UDE 0.538244816501366
Handling cluster '3' with mean UDE 1.43530796540674
Handling cluster '4' with mean UDE 0.632684489354434
clustersDeltaExpression - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'
Log Fold Change Analysis - DONE
findClustersMarkers - DONE
findClustersMarkers - START
Differential Expression Analysis - START
* DEA on cluster '1'
* DEA on cluster '2'
* DEA on cluster '3'
* DEA on cluster '4'
Differential Expression Analysis - DONE
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.20998115359079
Handling cluster '2' with mean UDE 0.538244816501366
Handling cluster '3' with mean UDE 1.43530796540674
Handling cluster '4' with mean UDE 0.632684489354434
clustersDeltaExpression - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'
Log Fold Change Analysis - DONE
findClustersMarkers - DONE
[1] "1"
Asked to drop 0 genes and 879 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [321] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0501708984375 | max: 14.515625 | % negative: 8.5
Only analysis elapsed time: 2.8094482421875
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.69694519042969
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00588083267211914
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0309937000274658
Estimating genes' coex
Calculate genes' coex elapsed time: 0.83292555809021
Total calculations elapsed time: 3.56674528121948
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.376136302948
Total elapsed time: 8.13958787918091
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
[1] "3"
Asked to drop 0 genes and 847 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [353] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.038818359375 | max: 11.109375 | % negative: 5
Only analysis elapsed time: 2.51943826675415
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.5739893913269
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00563240051269531
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.034942626953125
Estimating genes' coex
Calculate genes' coex elapsed time: 0.865890979766846
Total calculations elapsed time: 3.48045539855957
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.30081391334534
Total elapsed time: 7.56739044189453
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [10] genes and [20] cells
Initializing `COTAN` meta-data
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 2.82727527618408
Cotan genes' coex estimation started
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.42398142814636
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.0058283805847168
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0453650951385498
Estimating genes' coex
Calculate genes' coex elapsed time: 0.684298515319824
Total calculations elapsed time: 3.15947341918945
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 3.83610153198242
Total elapsed time: 7.49189448356628
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
S matrix sorted
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
Calculating gene co-expression space - DONE
Establishing gene clusters - START
Calculating gene co-expression space - START
Using S
Calculating S: START
Calculating S: DONE
calculating PValues: START
Get p-values on a set of genes on columns and genome wide on rows
calculating PValues: DONE
Number of selected secondary markers: 109
Calculating S: START
Calculating S: DONE
S matrix sorted
Number of columns (V set - secondary markers): 109
Number of rows (U set): 60
Calculating gene co-expression space - DONE
Establishing gene clusters - DONE
Initializing `COTAN` meta-data
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Cotan genes' coex estimation not requested
Total elapsed time: 4.83952498435974
Differential Expression Analysis - START
* DEA on cluster '1'
* DEA on cluster '2'
* DEA on cluster '3'
* DEA on cluster '4'
Differential Expression Analysis - DONE
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
* Analysis of cluster: '3'
* Analysis of cluster: '4'
Log Fold Change Analysis - DONE
clustersDeltaExpression - START
Handling cluster '1' with mean UDE 1.43530796540674
Handling cluster '2' with mean UDE 0.640931107489519
Handling cluster '3' with mean UDE 0.546546914955575
Handling cluster '4' with mean UDE 1.22034802329657
clustersDeltaExpression - DONE
In group G1 there are 3 detected over 3 genes
In group G2 there are 2 detected over 2 genes
In group G3 there are 5 detected over 5 genes
Merging cells' uniform clustering: START
Start merging nearest clusters: iteration 1
Differential Expression Analysis - START
* DEA on cluster '1'
* DEA on cluster '2'
* DEA on cluster '3'
* DEA on cluster '4'
Differential Expression Analysis - DONE
Clusters pairs for merging:
c("1", "2") c("3", "4") c("2", "3") c("2", "4") c("1", "3") c("1", "4")
*1_2-merge
Asked to drop 0 genes and 626 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [574] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333
Only analysis elapsed time: 2.75593590736389
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.58962321281433
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00709748268127441
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0395708084106445
Estimating genes' coex
Calculate genes' coex elapsed time: 0.863422393798828
Total calculations elapsed time: 3.49971389770508
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.443115234375
Total elapsed time: 7.93419098854065
Checking uniformity for the cluster '1_2-merge' with 574 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge, with size 574, is uniform
0.67% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.4297
Clusters 1 and 2 can be merged
*3_4-merge
Asked to drop 0 genes and 574 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [626] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667
Only analysis elapsed time: 2.67764616012573
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.49339652061462
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00628662109375
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.034550666809082
Estimating genes' coex
Calculate genes' coex elapsed time: 0.749525547027588
Total calculations elapsed time: 3.28375935554504
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.17306017875671
Total elapsed time: 7.63738703727722
Checking uniformity for the cluster '3_4-merge' with 626 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 3_4-merge, with size 626, is uniform
1% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.4544
Clusters 3 and 4 can be merged
*Clusters 2 or 3 is now missing due to previous merges: skip.
*Clusters 2 or 4 is now missing due to previous merges: skip.
*Clusters 1 or 3 is now missing due to previous merges: skip.
*Clusters 1 or 4 is now missing due to previous merges: skip.
Executed 2 merges out of 6
Start merging nearest clusters: iteration 2
Differential Expression Analysis - START
* DEA on cluster '1_2-merge'
* DEA on cluster '3_4-merge'
Differential Expression Analysis - DONE
Clusters pairs for merging:
c("1_2-merge", "3_4-merge")
*1_2-merge_3_4-merge-merge
Asked to drop no genes or cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [1200] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: 0.2197265625 | max: 6.08056640625 | % negative: 0
Only analysis elapsed time: 3.04810547828674
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.9784574508667
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00670862197875977
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0459659099578857
Estimating genes' coex
Calculate genes' coex elapsed time: 0.954309701919556
Total calculations elapsed time: 3.9854416847229
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.78822875022888
Total elapsed time: 8.75195956230164
Checking uniformity for the cluster '1_2-merge_3_4-merge-merge' with 1200 cells
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
GDI plot
Removed 0 low GDI genes (such as the fully-expressed) in GDI plot
Cluster 1_2-merge_3_4-merge-merge, with size 1200, is not uniform
22.17% of the genes is above the given GDI threshold 1.46
GDI 99% quantile is at 1.6405
Merging clusters 1_2-merge and 3_4-merge results in a too high GDI
None of the 1 nearest cluster pairs could be merged
The final merged clusterization contains [2] different clusters: 1_2-merge, 3_4-merge
Differential Expression Analysis - START
* DEA on cluster '1'
* DEA on cluster '2'
Differential Expression Analysis - DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Merging cells' uniform clustering: DONE
Applied reordering to clusterization is:
1 -> 1, 2 -> 2
Log Fold Change Analysis - START
* Analysis of cluster: '1'
* Analysis of cluster: '2'
Log Fold Change Analysis - DONE
Asked to drop 0 genes and 626 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [574] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.0340576171875 | max: 10.4375 | % negative: 4.33333333333333
Only analysis elapsed time: 2.47004795074463
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.43402194976807
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00666332244873047
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0400042533874512
Estimating genes' coex
Calculate genes' coex elapsed time: 0.768025636672974
Total calculations elapsed time: 3.24871516227722
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.03612661361694
Total elapsed time: 7.34277319908142
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
Asked to drop 0 genes and 574 cells
Cotan analysis functions started
Genes/cells selection done: dropped [0] genes and [0] cells
Working on [600] genes and [626] cells
Estimate dispersion: START
Effective number of cores used: 1
Executing 1 genes batches from [1:600] to [1:600]
Estimate dispersion: DONE
dispersion | min: -0.03839111328125 | max: 17.40625 | % negative: 6.66666666666667
Only analysis elapsed time: 2.70237016677856
Cotan genes' coex estimation started
While trying to load the `torch` library Error in doTryCatch(return(expr), name, parentenv, handler): The `torch` library is installed but the required additional libraries are not avalable yet
Calculate genes' coex (legacy): START
Retrieving expected genes' contingency table
calculating NN.. done
calculating NY..YN..YY..t().. done
Expected genes' contingency table elapsed time: 2.68932867050171
Calculating genes' coex normalization factor
Calculate genes' normalization factor elapsed time: 0.00660324096679688
Retrieving observed genes' yes/yes contingency table
calculating YY.. done
Observed genes' contingency table elapsed time: 0.0366482734680176
Estimating genes' coex
Calculate genes' coex elapsed time: 0.705569744110107
Total calculations elapsed time: 3.43814992904663
Calculate genes' coex (legacy): DONE
Only genes' coex elapsed time: 4.17025518417358
Total elapsed time: 7.67209959030151
Calculate GDI dataframe: START
Using S
Calculating S: START
Calculating S: DONE
S matrix sorted
Calculate GDI dataframe: DONE
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 433 ]
>
> proc.time()
user system elapsed
581.703 4.395 580.556
COTAN.Rcheck/COTAN-Ex.timings
| name | user | system | elapsed | |
| COTAN-Legacy | 0.003 | 0.000 | 0.004 | |
| COTANObjectCreation | 7.803 | 0.251 | 7.742 | |
| CalculatingCOEX | 45.899 | 0.778 | 45.311 | |
| ClustersList | 0.004 | 0.004 | 0.008 | |
| GenesStatistics | 8.682 | 0.232 | 8.472 | |
| HandleMetaData | 0.082 | 0.012 | 0.094 | |
| HandlingClusterizations | 18.006 | 0.235 | 18.148 | |
| HandlingConditions | 0.091 | 0.000 | 0.091 | |
| HeatmapPlots | 38.588 | 0.659 | 38.246 | |
| LoggingFunctions | 0.000 | 0.003 | 0.003 | |
| ParametersEstimations | 21.839 | 0.240 | 22.061 | |
| RawDataCleaning | 6.339 | 0.136 | 6.398 | |
| RawDataGetters | 0.079 | 0.000 | 0.079 | |
| UniformClusters | 132.319 | 0.562 | 131.076 | |
| getColorsVector | 0.001 | 0.000 | 0.001 | |