##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:EWCE.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings EWCE_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/EWCE.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘EWCE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘EWCE’ version ‘1.18.0’
* 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 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 ... 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 ... NOTE
checkRd: (-1) compute_gene_scores.Rd:42: Lost braces in \itemize; meant \describe ?
checkRd: (-1) compute_gene_scores.Rd:43: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drop_uninformative_genes.Rd:186-187: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drop_uninformative_genes.Rd:188-189: Lost braces in \itemize; meant \describe ?
checkRd: (-1) drop_uninformative_genes.Rd:190-192: Lost braces in \itemize; meant \describe ?
* 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 ... NOTE
Documented arguments not in \usage in Rd file 'get_exp_data_for_bootstrapped_genes.Rd':
  ‘full_results’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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              19.525  0.375  20.558
merged_ewce                                17.366  1.864  20.252
generate_bootstrap_plots_for_transcriptome 14.650  0.239  16.752
filter_genes_without_1to1_homolog          13.784  0.550  14.327
filter_nonorthologs                        12.836  0.302  14.157
generate_bootstrap_plots                   11.745  0.424  12.908
sct_normalize                               9.047  1.457  10.570
ewce_expression_data                       10.021  0.260  10.623
check_ewce_genelist_inputs                  9.776  0.192  11.786
bootstrap_enrichment_test                   9.395  0.204   9.980
merge_ctd                                   6.808  0.692   7.807
standardise_ctd                             7.149  0.291   7.633
filter_ctd_genes                            6.331  0.120   7.278
add_res_to_merging_list                     5.140  0.198   7.900
bin_specificity_into_quantiles              5.067  0.127   5.274
merge_sce                                   4.566  0.533   6.246
fix_bad_mgi_symbols                         4.563  0.376   6.864
generate_celltype_data                      4.156  0.308   6.336
ctd_to_sce                                  3.436  0.045   5.331
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL EWCE
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘EWCE’ ...
** this is package ‘EWCE’ version ‘1.18.0’
** 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)

R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 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.

> library(testthat)
> library(EWCE)
Loading required package: RNOmni
> 
> test_check("EWCE")
1 core(s) assigned as workers (71 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 ==>  /tmp/RtmpIfuuGo/ctd_testthat.rda
1 core(s) assigned as workers (71 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 ==>  /tmp/RtmpIfuuGo/ctd_testthat.rda
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 core(s) assigned as workers (71 reserved).
=== START walking on horizontal strip 1/5 ===
  | processing <4159 x 3005> block from grid position [[1/5, 1/1]] ... ok
=== DONE walking on horizontal strip 1/5 ===
--- START finalizing result for horizonal strip 1/5 ---
  | result is a <4159 x 7> matrix --> returning as-is
--- DONE finalizing result for horizonal strip 1/5 ---

=== START walking on horizontal strip 2/5 ===
  | processing <4159 x 3005> block from grid position [[2/5, 1/1]] ... ok
=== DONE walking on horizontal strip 2/5 ===
--- START finalizing result for horizonal strip 2/5 ---
  | result is a <4159 x 7> matrix --> returning as-is
--- DONE finalizing result for horizonal strip 2/5 ---

=== START walking on horizontal strip 3/5 ===
  | processing <4159 x 3005> block from grid position [[3/5, 1/1]] ... ok
=== DONE walking on horizontal strip 3/5 ===
--- START finalizing result for horizonal strip 3/5 ---
  | result is a <4159 x 7> matrix --> returning as-is
--- DONE finalizing result for horizonal strip 3/5 ---

=== START walking on horizontal strip 4/5 ===
  | processing <4159 x 3005> block from grid position [[4/5, 1/1]] ... ok
=== DONE walking on horizontal strip 4/5 ===
--- START finalizing result for horizonal strip 4/5 ---
  | result is a <4159 x 7> matrix --> returning as-is
--- DONE finalizing result for horizonal strip 4/5 ---

=== START walking on horizontal strip 5/5 ===
  | processing <3336 x 3005> block from grid position [[5/5, 1/1]] ... ok
=== DONE walking on horizontal strip 5/5 ===
--- START finalizing result for horizonal strip 5/5 ---
  | result is a <3336 x 7> matrix --> returning as-is
--- DONE finalizing result for horizonal strip 5/5 ---

=== FINAL STEP ===
  | rbind()'ing strip results (5 matrices) together ... ok
=== DONE ===

Converting to sparse matrix.
Converting to sparse matrix.
1 core(s) assigned as workers (71 reserved).
=== START walking on vertical strip 1/1 ===
  | processing <4159 x 3005> block from grid position [[1/5, 1/1]] ... ok
  | processing <4159 x 3005> block from grid position [[2/5, 1/1]] ... ok
  | processing <4159 x 3005> block from grid position [[3/5, 1/1]] ... ok
  | processing <4159 x 3005> block from grid position [[4/5, 1/1]] ... ok
  | processing <3336 x 3005> block from grid position [[5/5, 1/1]] ... ok
=== DONE walking on vertical strip 1/1 ===

=== START walking on vertical strip 1/1 ===
  | processing <4159 x 3005> block from grid position [[1/5, 1/1]] ... ok
  | processing <4159 x 3005> block from grid position [[2/5, 1/1]] ... ok
  | processing <4159 x 3005> block from grid position [[3/5, 1/1]] ... ok
  | processing <4159 x 3005> block from grid position [[4/5, 1/1]] ... ok
  | processing <3336 x 3005> block from grid position [[5/5, 1/1]] ... ok
=== DONE walking on vertical strip 1/1 ===

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 10 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 34.69784 secs
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 (71 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 --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_noText____VignetteGraphs.pdf
Saving plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtgene____VignetteGraphs.pdf
Saving plot --> /tmp/RtmpIfuuGo/BootstrapPlots/bootDists____VignetteGraphs.pdf
Saving plot --> /tmp/RtmpIfuuGo/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 (71 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 (71 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 --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____endothelial_mural.pdf
endothelial_mural : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____endothelial_mural.pdf
endothelial_mural : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____endothelial_mural.pdf
$plot1

$plot2

microglia : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____microglia.pdf
microglia : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____microglia.pdf
microglia : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____microglia.pdf
$plot1

$plot2

oligodendrocytes : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____oligodendrocytes.pdf
oligodendrocytes : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____oligodendrocytes.pdf
oligodendrocytes : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____oligodendrocytes.pdf
$plot1

$plot2

interneurons : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____interneurons.pdf
interneurons : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____interneurons.pdf
interneurons : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____interneurons.pdf
$plot1

$plot2

astrocytes_ependymal : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____astrocytes_ependymal.pdf
astrocytes_ependymal : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____astrocytes_ependymal.pdf
astrocytes_ependymal : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____astrocytes_ependymal.pdf
$plot1

$plot2

pyramidal_CA1 : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____pyramidal_CA1.pdf
pyramidal_CA1 : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____pyramidal_CA1.pdf
pyramidal_CA1 : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirUp___examples____pyramidal_CA1.pdf
$plot1

$plot2

pyramidal_SS : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_noText_thresh250__dirUp___examples____pyramidal_SS.pdf
pyramidal_SS : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSym_thresh250__dirUp___examples____pyramidal_SS.pdf
pyramidal_SS : Saving bootstrap plot --> /tmp/RtmpIfuuGo/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 --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____interneurons.pdf
interneurons : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____interneurons.pdf
interneurons : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____interneurons.pdf
$plot1

$plot2

pyramidal_SS : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____pyramidal_SS.pdf
pyramidal_SS : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____pyramidal_SS.pdf
pyramidal_SS : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____pyramidal_SS.pdf
$plot1

$plot2

pyramidal_CA1 : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____pyramidal_CA1.pdf
pyramidal_CA1 : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____pyramidal_CA1.pdf
pyramidal_CA1 : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____pyramidal_CA1.pdf
$plot1

$plot2

oligodendrocytes : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____oligodendrocytes.pdf
oligodendrocytes : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____oligodendrocytes.pdf
oligodendrocytes : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____oligodendrocytes.pdf
$plot1

$plot2

microglia : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____microglia.pdf
microglia : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____microglia.pdf
microglia : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____microglia.pdf
$plot1

$plot2

endothelial_mural : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____endothelial_mural.pdf
endothelial_mural : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____endothelial_mural.pdf
endothelial_mural : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSymBIG_thresh250__dirDown___examples____endothelial_mural.pdf
$plot1

$plot2

astrocytes_ependymal : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_noText_thresh250__dirDown___examples____astrocytes_ependymal.pdf
astrocytes_ependymal : Saving bootstrap plot --> /tmp/RtmpIfuuGo/BootstrapPlots/qqplot_wtGSym_thresh250__dirDown___examples____astrocytes_ependymal.pdf
astrocytes_ependymal : Saving bootstrap plot --> /tmp/RtmpIfuuGo/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 (71 reserved).
1 core(s) assigned as workers (71 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
Saving _problems/test-bootstrap_enrichment_test_2-62.R
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
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 (71 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 0.9643607 secs
1 core(s) assigned as workers (71 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 ==>  /tmp/RtmpIfuuGo/ctd_kiCortexOnly.rda
1 core(s) assigned as workers (71 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 ==>  /tmp/RtmpIfuuGo/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 (71 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 (71 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 (71 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 (71 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 (71 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 (71 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
Warning: sctSpecies_origin not provided. Setting to 'mouse' by default.
1 core(s) assigned as workers (71 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 0.7929554 secs
1 core(s) assigned as workers (71 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 ==>  /tmp/RtmpIfuuGo/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 78596723 bytes (75.0 MB)