Alan Murphy
| Snapshot Date: 2023-10-04 14:05:06 -0400 (Wed, 04 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/EWCE |
| git_branch: devel |
| git_last_commit: 5a472f8 |
| git_last_commit_date: 2023-08-29 05:27:30 -0400 (Tue, 29 Aug 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-10-05 11:40:26 -0400 (Thu, 05 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4405 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4424 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4410 |
| 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 668/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EWCE 1.9.3 (landing page) Alan Murphy
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | TIMEOUT | ||||||||||
|
To the developers/maintainers of the EWCE package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EWCE.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: EWCE |
| Version: 1.9.3 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:EWCE.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings EWCE_1.9.3.tar.gz |
| StartedAt: 2023-10-05 04:33:06 -0000 (Thu, 05 Oct 2023) |
| EndedAt: 2023-10-05 05:13:07 -0000 (Thu, 05 Oct 2023) |
| EllapsedTime: 2400.4 seconds |
| RetCode: None |
| Status: TIMEOUT |
| CheckDir: EWCE.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:EWCE.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings EWCE_1.9.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/EWCE.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘EWCE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EWCE’ version ‘1.9.3’
* 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 ‘EWCE’ 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 R 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
controlled_geneset_enrichment 30.566 0.826 36.820
merged_ewce 24.559 0.817 28.221
generate_bootstrap_plots_for_transcriptome 18.398 0.332 21.201
filter_nonorthologs 16.986 0.438 18.899
generate_bootstrap_plots 16.433 0.315 18.939
filter_genes_without_1to1_homolog 15.986 0.333 17.696
sct_normalize 13.444 0.308 15.280
bootstrap_enrichment_test 13.162 0.200 17.055
ewce_expression_data 12.900 0.424 15.668
check_ewce_genelist_inputs 11.732 0.134 17.886
standardise_ctd 9.785 0.203 11.496
merge_ctd 9.549 0.328 10.930
filter_ctd_genes 8.255 0.251 10.529
add_res_to_merging_list 6.938 0.260 18.903
merge_sce 6.914 0.215 8.597
fix_bad_mgi_symbols 6.697 0.323 9.929
ctd_to_sce 5.635 0.125 943.959
generate_celltype_data 5.394 0.234 8.664
bin_columns_into_quantiles 5.341 0.120 6.456
bin_specificity_into_quantiles 5.353 0.108 7.852
plot_ctd 5.198 0.108 6.788
drop_uninformative_genes 5.027 0.222 6.682
merge_two_expfiles 4.053 0.315 5.876
get_celltype_table 3.808 0.155 5.460
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
4. └─ExperimentHub (local) .local(x, i, j = j, ...)
5. ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
6. │ └─base::eval(call, callEnv)
7. │ └─base::eval(call, callEnv)
8. └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
9. └─AnnotationHub (local) .local(x, i, j = j, ...)
10. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─value[[3L]](cond)
[ FAIL 3 | WARN 43 | SKIP 0 | PASS 112 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘EWCE.Rmd’ using ‘UTF-8’... OK
‘extended.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ...
EWCE.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL EWCE ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘EWCE’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (EWCE)
EWCE.Rcheck/tests/testthat.Rout.fail
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
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.
> library(testthat)
> library(EWCE)
Loading required package: RNOmni
>
> test_check("EWCE")
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Loading required namespace: ggdendro
+ Saving results ==> /home/biocbuild/tmp/Rtmp9gpP7O/ctd_testthat.rda
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> /home/biocbuild/tmp/Rtmp9gpP7O/ctd_testthat.rda
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
Converting to sparse matrix.
1 core(s) assigned as workers (31 reserved).
Processing block [[1/5, 1/1]] ... OK
Processing block [[2/5, 1/1]] ... OK
Processing block [[3/5, 1/1]] ... OK
Processing block [[4/5, 1/1]] ... OK
Processing block [[5/5, 1/1]] ... OK
Processing block [[1/5, 1/1]] ... OK
Processing block [[2/5, 1/1]] ... OK
Processing block [[3/5, 1/1]] ... OK
Processing block [[4/5, 1/1]] ... OK
Processing block [[5/5, 1/1]] ... OK
Loading required namespace: sctransform
Converting to sparse matrix.
Calculating cell attributes from input UMI matrix: log_umi
Variance stabilizing transformation of count matrix of size 17757 by 3005
Model formula is y ~ log_umi
Get Negative Binomial regression parameters per gene
Using 2000 genes, 3005 cells
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Found 12 outliers - those will be ignored in fitting/regularization step
Second step: Get residuals using fitted parameters for 17757 genes
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Calculating gene attributes
Wall clock passed: Time difference of 1.065673 mins
Computing corrected UMI count matrix
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see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
+ <2 non-zero quantile bins detected in column. Assigning these values to default quantile ( 20 )
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 core(s) assigned as workers (31 reserved).
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
17 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
2 significant cell type enrichment results @ q<0.05 :
CellType annotLevel p fold_change sd_from_mean q
1 microglia 1 0 1.820518 2.409647 0
2 astrocytes_ependymal 1 0 1.357308 1.995351 0
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Standardising sct_data.
Aligning celltype names with standardise_ctd format.
Checking gene list inputs.
2 celltype(s) remain @ <= 0.05
Resampling random genes.
Generating bootstrap plot for 2 celltype(s).
Saving plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_noText____VignetteGraphs.pdf
Saving plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtgene____VignetteGraphs.pdf
Saving plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/bootDists____VignetteGraphs.pdf
Saving plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/bootDists_LOG____VignetteGraphs.pdf
$plot1
$plot2
$plot3
$plot4
Warning: genelistSpecies not provided. Setting to 'human' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
15,259 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Returning gene_map as dictionary
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
13,243 / 15,259 (87%)
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
Returning 19,129 unique genes from entire human genome.
Using intersect between background gene lists: 16,482 genes.
Standardising sct_data.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
6 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
1 significant cell type enrichment results @ q<0.05 :
CellType annotLevel p fold_change sd_from_mean q
1 endothelial_mural 1 0 1.960864 4.367242 0
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
5 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
2 significant cell type enrichment results @ q<0.05 :
CellType annotLevel p fold_change sd_from_mean q
1 interneurons 1 0 1.742023 3.948853 0
2 pyramidal_SS 1 0 1.991393 3.203248 0
Warning: genelistSpecies not provided. Setting to 'human' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Aligning celltype names with standardise_ctd format.
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
15,259 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Returning gene_map as dictionary
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
13,243 / 15,259 (87%)
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
Returning 19,129 unique genes from entire human genome.
Using intersect between background gene lists: 16,482 genes.
Standardising sct_data.
Using 1st column of tt as gene column: HGNC.symbol
Generating exp data for bootstrap genes.
Converting data for bootstrap tests to sparse matrices.
endothelial_mural : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____endothelial_mural.pdf
endothelial_mural : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____endothelial_mural.pdf
endothelial_mural : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____endothelial_mural.pdf
$plot1
$plot2
microglia : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____microglia.pdf
microglia : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____microglia.pdf
microglia : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____microglia.pdf
$plot1
$plot2
oligodendrocytes : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____oligodendrocytes.pdf
oligodendrocytes : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____oligodendrocytes.pdf
oligodendrocytes : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____oligodendrocytes.pdf
$plot1
$plot2
interneurons : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____interneurons.pdf
interneurons : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____interneurons.pdf
interneurons : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____interneurons.pdf
$plot1
$plot2
astrocytes_ependymal : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____astrocytes_ependymal.pdf
astrocytes_ependymal : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____astrocytes_ependymal.pdf
astrocytes_ependymal : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____astrocytes_ependymal.pdf
$plot1
$plot2
pyramidal_CA1 : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____pyramidal_CA1.pdf
pyramidal_CA1 : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____pyramidal_CA1.pdf
pyramidal_CA1 : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____pyramidal_CA1.pdf
$plot1
$plot2
pyramidal_SS : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____pyramidal_SS.pdf
pyramidal_SS : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____pyramidal_SS.pdf
pyramidal_SS : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____pyramidal_SS.pdf
$plot1
$plot2
Generating exp data for bootstrap genes.
Converting data for bootstrap tests to sparse matrices.
interneurons : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____interneurons.pdf
interneurons : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____interneurons.pdf
interneurons : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____interneurons.pdf
$plot1
$plot2
pyramidal_SS : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____pyramidal_SS.pdf
pyramidal_SS : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____pyramidal_SS.pdf
pyramidal_SS : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____pyramidal_SS.pdf
$plot1
$plot2
pyramidal_CA1 : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____pyramidal_CA1.pdf
pyramidal_CA1 : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____pyramidal_CA1.pdf
pyramidal_CA1 : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____pyramidal_CA1.pdf
$plot1
$plot2
oligodendrocytes : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____oligodendrocytes.pdf
oligodendrocytes : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____oligodendrocytes.pdf
oligodendrocytes : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____oligodendrocytes.pdf
$plot1
$plot2
microglia : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____microglia.pdf
microglia : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____microglia.pdf
microglia : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____microglia.pdf
$plot1
$plot2
endothelial_mural : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____endothelial_mural.pdf
endothelial_mural : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____endothelial_mural.pdf
endothelial_mural : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____endothelial_mural.pdf
$plot1
$plot2
astrocytes_ependymal : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____astrocytes_ependymal.pdf
astrocytes_ependymal : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____astrocytes_ependymal.pdf
astrocytes_ependymal : Saving bootstrap plot --> /home/biocbuild/tmp/Rtmp9gpP7O/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____astrocytes_ependymal.pdf
$plot1
$plot2
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
22 genes extracted.
Converting human ==> mouse orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Checking for genes without orthologs in mouse.
Extracting genes from input_gene.
17 genes extracted.
Extracting genes from ortholog_gene.
17 genes extracted.
Checking for genes without 1:1 orthologs.
Filtering gene_df with gene_map
Returning gene_map as dictionary
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
5 / 22 (23%)
Total genes remaining after convert_orthologs :
17 / 22 (77%)
1 core(s) assigned as workers (31 reserved).
1 core(s) assigned as workers (31 reserved).
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Standardising CellTypeDataset
Checking gene list inputs.
Running with gene size control.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Retrieving all genes using: gprofiler
Retrieving all organisms available in gprofiler.
Using stored `gprofiler_orgs`.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: hsapiens
Gene table with 62,663 rows retrieved.
Returning all 62,663 genes from human.
62,663 human Ensembl IDs and 40,835 human Gene Symbols imported.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Controlled bootstrapping network generated.
17 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
1 significant cell type enrichment results @ q<0.05 :
CellType annotLevel p fold_change sd_from_mean q
1 microglia 1 0 2.120161 4.300734 0
1 core(s) assigned as workers (31 reserved).
Returning 15,604 unique genes from the user-supplied bg.
Standardising CellTypeDataset
Checking gene list inputs.
Converting gene list input to standardised human genes.
1 core(s) assigned as workers (31 reserved).
Returning 15,589 unique genes from the user-supplied bg.
Standardising CellTypeDataset
Checking gene list inputs.
Converting gene list input to standardised human genes.
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
22 genes extracted.
Converting human ==> rat orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Checking for genes without orthologs in rat.
Extracting genes from input_gene.
18 genes extracted.
Extracting genes from ortholog_gene.
18 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 2 genes that have multiple input_gene per ortholog_gene (many:1).
Filtering gene_df with gene_map
Returning gene_map as dictionary
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
7 / 22 (32%)
Total genes remaining after convert_orthologs :
15 / 22 (68%)
1 core(s) assigned as workers (31 reserved).
Generating gene background for mouse x rat ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- rat
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Gene table with 20,616 rows retrieved.
Returning all 20,616 genes from rat.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
20,616 genes extracted.
Converting rat ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: rat
Common name mapping found for rat
1 organism identified from search: 10116
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
16,989 genes extracted.
Extracting genes from ortholog_gene.
16,989 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 122 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 607 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,813 / 20,616 (23%)
Total genes remaining after convert_orthologs :
15,803 / 20,616 (77%)
--
=========== REPORT SUMMARY ===========
15,803 / 20,616 (76.65%) target_species genes remain after ortholog conversion.
15,803 / 19,129 (82.61%) reference_species genes remain after ortholog conversion.
15,450 intersect background genes used.
Standardising CellTypeDataset
Checking gene list inputs.
Converting gene list input to standardised human genes.
Running without gene size control.
15 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
1 significant cell type enrichment results @ q<0.05 :
CellType annotLevel p fold_change sd_from_mean q
1 microglia 1 0 2.156018 4.415353 0
Standardising CellTypeDataset
Found 5 matrix types across 2 CTD levels.
Processing level: 1
Processing level: 2
1 core(s) assigned as workers (31 reserved).
Generating gene background for monkey x mouse ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- monkey
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: monkey
Common name mapping found for monkey
1 organism identified from search: 9544
Gene table with 16,843 rows retrieved.
Returning all 16,843 genes from monkey.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
16,843 genes extracted.
Converting monkey ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: monkey
Common name mapping found for monkey
1 organism identified from search: 9544
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
15,675 genes extracted.
Extracting genes from ortholog_gene.
15,675 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 197 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 215 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
1,726 / 16,816 (10%)
Total genes remaining after convert_orthologs :
15,090 / 16,816 (90%)
--
=========== REPORT SUMMARY ===========
15,077 / 16,816 (89.66%) target_species genes remain after ortholog conversion.
15,077 / 19,129 (78.82%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
13,875 intersect background genes used.
Standardising CellTypeDataset
Checking gene list inputs.
Converting gene list input to standardised human genes.
Running without gene size control.
11 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
0 significant cell type enrichment results @ q<0.05 :
1 core(s) assigned as workers (31 reserved).
Generating gene background for godzilla x mouse ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- godzilla
1 core(s) assigned as workers (31 reserved).
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Standardising CellTypeDataset
Checking gene list inputs.
1 core(s) assigned as workers (31 reserved).
Returning 15,604 unique genes from the user-supplied bg.
Standardising CellTypeDataset
Checking gene list inputs.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Check 1000Check 3005
Warning: sctSpecies not provided. Setting to 'mouse' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
Checking for non-expressed genes.
Checking for cells with no expressed genes.
DGE:: Limma...
248 / 1,000 genes dropped @ DGE adj_pval_thresh < 1e-05
Time difference of 1.427751 secs
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> /home/biocbuild/tmp/Rtmp9gpP7O/ctd_kiCortexOnly.rda
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> /home/biocbuild/tmp/Rtmp9gpP7O/ctd_kiCortexOnly.rda
Loading precomputed example bootstrap results.
Aligning celltype names with standardise_ctd format.
7 signficiant enrichment results @ bonferroni < 0.05
14.3% of hits are of the target cell type.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
Standardising CellTypeDataset
Found 5 matrix types across 2 CTD levels.
Processing level: 1
Processing level: 2
Generating controlled bootstrap gene sets.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Warning: genelistSpecies not provided. Setting to 'human' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
15,259 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Returning gene_map as dictionary
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
13,243 / 15,259 (87%)
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
Returning 19,129 unique genes from entire human genome.
Using intersect between background gene lists: 16,482 genes.
Standardising sct_data.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
28 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
1 significant cell type enrichment results @ q<0.05 :
CellType annotLevel p fold_change sd_from_mean q
1 endothelial_mural 1 0 1.628635 4.684982 0
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
26 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
0 significant cell type enrichment results @ q<0.05 :
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Warning: genelistSpecies not provided. Setting to 'human' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
15,259 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Returning gene_map as dictionary
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
13,243 / 15,259 (87%)
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
Returning 19,129 unique genes from entire human genome.
Using intersect between background gene lists: 16,482 genes.
Standardising sct_data.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
10 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
0 significant cell type enrichment results @ q<0.05 :
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
8 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
1 significant cell type enrichment results @ q<0.05 :
CellType annotLevel p fold_change sd_from_mean q
1 pyramidal_CA1 1 0 1.318978 1.682404 0
Warning: genelistSpecies not provided. Setting to 'human' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
Preparing gene_df.
character format detected.
Converting to data.frame
Extracting genes from input_gene.
15,259 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
13,416 genes extracted.
Extracting genes from ortholog_gene.
13,416 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 46 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 56 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Returning gene_map as dictionary
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
2,016 / 15,259 (13%)
Total genes remaining after convert_orthologs :
13,243 / 15,259 (87%)
Generating gene background for mouse x human ==> human
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- mouse
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Gene table with 21,207 rows retrieved.
Returning all 21,207 genes from mouse.
--
--
Preparing gene_df.
data.frame format detected.
Extracting genes from Gene.Symbol.
21,207 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
17,355 genes extracted.
Extracting genes from ortholog_gene.
17,355 genes extracted.
Checking for genes without 1:1 orthologs.
Dropping 131 genes that have multiple input_gene per ortholog_gene (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
Gathering ortholog reports.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
-- human
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
--
=========== REPORT SUMMARY ===========
19,129 / 19,129 (100%) target_species genes remain after ortholog conversion.
19,129 / 19,129 (100%) reference_species genes remain after ortholog conversion.
16,482 intersect background genes used.
Retrieving all genes using: homologene.
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Gene table with 19,129 rows retrieved.
Returning all 19,129 genes from human.
Returning 19,129 unique genes from entire human genome.
Using intersect between background gene lists: 16,482 genes.
Standardising sct_data.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
11 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
0 significant cell type enrichment results @ q<0.05 :
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Running without gene size control.
9 hit gene(s) remain after filtering.
Computing gene scores.
Using previously sampled genes.
Computing gene counts.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
0 significant cell type enrichment results @ q<0.05 :
Loading precomputed example bootstrap results.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Filtering CTD to 100 genes.
level: 1
Found 5 matrix types across 1 CTD levels.
- mean_exp
- median_exp
- specificity
- median_specificity
- specificity_quantiles
level: 2
Found 5 matrix types across 1 CTD levels.
- mean_exp
- median_exp
- specificity
- median_specificity
- specificity_quantiles
Standardising CellTypeDataset
Found 5 matrix types across 2 CTD levels.
Processing level: 1
Processing level: 2
Filtering CTD to 100 genes.
level: level_1
Found 5 matrix types across 1 CTD levels.
- mean_exp
- median_exp
- specificity
- median_specificity
- specificity_quantiles
level: level_2
Found 5 matrix types across 1 CTD levels.
- mean_exp
- median_exp
- specificity
- median_specificity
- specificity_quantiles
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Check 1000Check 3005
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
Checking for non-expressed genes.
Checking for cells with no expressed genes.
DGE:: Limma...
248 / 1,000 genes dropped @ DGE adj_pval_thresh < 1e-05
Time difference of 1.382731 secs
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> /home/biocbuild/tmp/Rtmp9gpP7O/ctd_kiCortexOnly.rda
+ Processing level 1 ...
Processing mean_exp
Processing specificity
Processing specificity_quantiles
+ Processing level 2 ...
Processing mean_exp
Processing specificity
Processing specificity_quantiles
No input_species provided. Setting to 'mouse'
+ Processing level 1 ...
Processing mean_exp
Processing specificity
Processing specificity_quantiles
+ Processing level 2 ...
Processing mean_exp
Processing specificity
Processing specificity_quantiles
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
trying URL 'http://www.informatics.jax.org/downloads/reports/MRK_List2.rpt'
Content type 'unknown' length 82842174 bytes (79.0 MB)
=======
downloaded 11.4 MB
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 core(s) assigned as workers (31 reserved).
Preparing gene_df.
Dense matrix format detected.
Extracting genes from rownames.
100 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
91 genes extracted.
Extracting genes from ortholog_gene.
91 genes extracted.
Checking for genes without 1:1 orthologs.
Filtering gene_df with gene_map
Setting ortholog_gene to rownames.
Converting obj to sparseMatrix.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
9 / 100 (9%)
Total genes remaining after convert_orthologs :
91 / 100 (91%)
Converting to sparse matrix.
Converting to DelayedArray.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> /home/biocbuild/tmp/Rtmp9gpP7O/ctd_allKImouse.rda
+ Returning list of CTD file name, and the CTD itself.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Filtering by variance quantiles.
Converting to DelayedArray.
120 / 300 genes dropped @ DGE min_variance_quantile >= 5
Converting to sparse matrix.
Calculating cell attributes from input UMI matrix: log_umi
Variance stabilizing transformation of count matrix of size 300 by 3005
Model formula is y ~ log_umi
Get Negative Binomial regression parameters per gene
Using 300 genes, 3005 cells
|
| | 0%
|
|======================================================================| 100%
Found 2 outliers - those will be ignored in fitting/regularization step
Second step: Get residuals using fitted parameters for 300 genes
|
| | 0%
|
|======================================================================| 100%
Calculating gene attributes
Wall clock passed: Time difference of 8.298218 secs
Computing corrected UMI count matrix
|
| | 0%
|
|======================================================================| 100%
Filtering by variance quantiles.
Converting to DelayedArray.
120 / 300 genes dropped @ DGE min_variance_quantile >= 5
Filtering by variance quantiles.
Converting to DelayedArray.
120 / 300 genes dropped @ DGE min_variance_quantile >= 5
Filtering by variance quantiles.
Converting to DelayedArray.
/ Reading and realizing block 1/1 ... OK
\ Processing it ... OK
120 / 300 genes dropped @ DGE min_variance_quantile >= 5
Retrieving all organisms available in homologene.
Returning table with all species.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
+ CTD ==> SingleCellExperiment
Converting level: level_1
Returning all possible matrix names.
Converting level: level_2
Returning all possible matrix names.
The assay 'mean_exp' will be used to determine the proportion of zeroes for each batch.
Converting CTD to merged SCEs
ctd1
+ CTD ==> SingleCellExperiment
Converting level: level_1
Returning all possible matrix names.
Converting level: level_2
Returning all possible matrix names.
ctd2
+ CTD ==> SingleCellExperiment
Converting level: level_1
Returning all possible matrix names.
Converting level: level_2
Returning all possible matrix names.
Merging SCE at level: 1
[1] "ctd1"
[1] "15259 x 7"
[1] "ctd2"
[1] "15259 x 7"
The assay 'mean_exp' will be used to determine the proportion of zeroes for each batch.
Merging SCE at level: 2
[1] "ctd1"
[1] "15259 x 48"
[1] "ctd2"
[1] "15259 x 48"
The assay 'mean_exp' will be used to determine the proportion of zeroes for each batch.
[1] "level_1"
[1] "level_2"
Saving SCE_merged ==> /home/biocbuild/tmp/Rtmp9gpP7O/merged/CTD_SCE_merged.union.rds
+ Must set `as_SCE=TRUE` in order to merge CTD.
+ Returning merged CTD.
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> /home/biocbuild/tmp/Rtmp9gpP7O/ctd_file22963f7b19522blevel_1.rda
+ Returning list of CTD file name, and the CTD itself.
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> /home/biocbuild/tmp/Rtmp9gpP7O/ctd_file22963f1e5b6951level_2.rda
+ Returning list of CTD file name, and the CTD itself.
see ?ewceData and browseVignettes('ewceData') for documentation
downloading 1 resources
retrieving 1 resource
loading from cache
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
[ FAIL 3 | WARN 43 | SKIP 0 | PASS 112 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-fix_bad_mgi_symbols.r:13:13'): method to remove/fix an expected set of genes ──
Error in `utils::download.file("http://www.informatics.jax.org/downloads/reports/MRK_List2.rpt",
destfile = tmp_mark_list)`: download from 'http://www.informatics.jax.org/downloads/reports/MRK_List2.rpt' failed
Backtrace:
▆
1. └─utils::download.file(...) at test-fix_bad_mgi_symbols.r:13:12
── Error ('test-merge_two_expfiles.R:5:9'): merging two expression files ───────
Error: failed to load resource
name: EH5381
title: cortex_mrna
reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
▆
1. └─ewceData::cortex_mrna() at test-merge_two_expfiles.R:5:8
2. ├─eh[["EH5381"]]
3. └─eh[["EH5381"]]
4. └─ExperimentHub (local) .local(x, i, j = j, ...)
5. ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
6. │ └─base::eval(call, callEnv)
7. │ └─base::eval(call, callEnv)
8. └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
9. └─AnnotationHub (local) .local(x, i, j = j, ...)
10. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─value[[3L]](cond)
── Error ('test-run_DGE.R:4:9'): DGE works ─────────────────────────────────────
Error: failed to load resource
name: EH5381
title: cortex_mrna
reason: error in evaluating the argument 'x' in selecting a method for function 'get': bad restore file magic number (file may be corrupted) -- no data loaded
Backtrace:
▆
1. └─ewceData::cortex_mrna() at test-run_DGE.R:4:8
2. ├─eh[["EH5381"]]
3. └─eh[["EH5381"]]
4. └─ExperimentHub (local) .local(x, i, j = j, ...)
5. ├─methods::callNextMethod(x, i, j, ..., force = force, verbose = verbose)
6. │ └─base::eval(call, callEnv)
7. │ └─base::eval(call, callEnv)
8. └─AnnotationHub (local) .nextMethod(x, i, j, ..., force = force, verbose = verbose)
9. └─AnnotationHub (local) .local(x, i, j = j, ...)
10. └─AnnotationHub:::.Hub_get1(x[idx], force = force, verbose = verbose)
11. └─base::tryCatch(...)
12. └─base (local) tryCatchList(expr, classes, parentenv, handlers)
13. └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
14. └─value[[3L]](cond)
[ FAIL 3 | WARN 43 | SKIP 0 | PASS 112 ]
Error: Test failures
Execution halted
EWCE.Rcheck/EWCE-Ex.timings
| name | user | system | elapsed | |
| add_res_to_merging_list | 6.938 | 0.260 | 18.903 | |
| bin_columns_into_quantiles | 5.341 | 0.120 | 6.456 | |
| bin_specificity_into_quantiles | 5.353 | 0.108 | 7.852 | |
| bootstrap_enrichment_test | 13.162 | 0.200 | 17.055 | |
| check_ewce_genelist_inputs | 11.732 | 0.134 | 17.886 | |
| check_percent_hits | 0.004 | 0.000 | 0.004 | |
| controlled_geneset_enrichment | 30.566 | 0.826 | 36.820 | |
| ctd_to_sce | 5.635 | 0.125 | 943.959 | |
| drop_uninformative_genes | 5.027 | 0.222 | 6.682 | |
| ewce_expression_data | 12.900 | 0.424 | 15.668 | |
| ewce_plot | 0.073 | 0.000 | 0.073 | |
| example_bootstrap_results | 0.001 | 0.000 | 0.001 | |
| example_transcriptome_results | 0.001 | 0.000 | 0.002 | |
| filter_ctd_genes | 8.255 | 0.251 | 10.529 | |
| filter_genes_without_1to1_homolog | 15.986 | 0.333 | 17.696 | |
| filter_nonorthologs | 16.986 | 0.438 | 18.899 | |
| fix_bad_hgnc_symbols | 1.280 | 0.072 | 2.812 | |
| fix_bad_mgi_symbols | 6.697 | 0.323 | 9.929 | |
| fix_celltype_names | 0 | 0 | 0 | |
| generate_bootstrap_plots | 16.433 | 0.315 | 18.939 | |
| generate_bootstrap_plots_for_transcriptome | 18.398 | 0.332 | 21.201 | |
| generate_celltype_data | 5.394 | 0.234 | 8.664 | |
| get_celltype_table | 3.808 | 0.155 | 5.460 | |
| list_species | 0.008 | 0.000 | 0.008 | |
| load_rdata | 0.001 | 0.000 | 0.001 | |
| merge_ctd | 9.549 | 0.328 | 10.930 | |
| merge_sce | 6.914 | 0.215 | 8.597 | |
| merge_two_expfiles | 4.053 | 0.315 | 5.876 | |
| merged_ewce | 24.559 | 0.817 | 28.221 | |
| plot_ctd | 5.198 | 0.108 | 6.788 | |
| sct_normalize | 13.444 | 0.308 | 15.280 | |
| standardise_ctd | 9.785 | 0.203 | 11.496 | |