Alan Murphy
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/EWCE |
| git_branch: master |
| git_last_commit: eaf2c4f |
| git_last_commit_date: 2022-02-09 14:10:46 -0400 (Wed, 09 Feb 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:28 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
To the developers/maintainers of the EWCE package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 613/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EWCE 1.3.3 (landing page) Alan Murphy
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: EWCE |
| Version: 1.3.3 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EWCE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings EWCE_1.3.3.tar.gz |
| StartedAt: 2022-03-17 19:03:10 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:17:28 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 858.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: EWCE.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:EWCE.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings EWCE_1.3.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/EWCE.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'EWCE/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'EWCE' version '1.3.3'
* 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 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 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
merged_ewce 20.76 1.32 22.66
controlled_geneset_enrichment 13.87 1.65 16.56
generate_bootstrap_plots_for_transcriptome 14.46 0.83 15.78
filter_nonorthologs 14.03 0.57 14.98
filter_genes_without_1to1_homolog 13.51 0.79 14.61
generate_bootstrap_plots 11.13 1.03 12.49
merge_ctd 10.79 0.91 11.85
sct_normalize 10.84 0.63 11.64
bootstrap_enrichment_test 10.58 0.65 11.56
ewce_expression_data 9.97 0.82 11.15
check_ewce_genelist_inputs 9.83 0.77 11.16
add_res_to_merging_list 7.18 1.53 9.94
standardise_ctd 6.10 0.37 6.77
fix_bad_mgi_symbols 4.76 0.75 6.05
merge_sce 4.98 0.28 5.57
bin_specificity_into_quantiles 4.59 0.33 5.11
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: OK
EWCE.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL EWCE
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'EWCE' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'EWCE'
finding HTML links ... done
EWCE-package html
add_res_to_merging_list html
assign_cores html
bin_columns_into_quantiles html
bin_specificity_into_quantiles html
bootstrap_enrichment_test html
bootstrap_plot html
calc_quantiles html
calculate_meanexp_for_level html
calculate_specificity_for_level html
cell_list_dist html
check_annotLevels html
check_args_for_bootstrap_plot_generation
html
check_bootstrap_args html
check_controlled_args html
check_ewce_expression_data_args html
check_ewce_genelist_inputs html
check_full_results html
check_generate_controlled_bootstrap_geneset
html
check_group_name html
check_nas html
check_numeric html
check_percent_hits html
check_sce html
check_species html
controlled_geneset_enrichment html
convert_new_ewce_to_old html
convert_old_ewce_to_new html
create_background_multilist html
create_list_network html
ctd_to_sce html
delayedarray_normalize html
drop_nonexpressed_cells html
drop_nonexpressed_genes html
drop_uninformative_genes html
dt_to_df html
ewce_expression_data html
ewce_plot html
example_bootstrap_results html
example_transcriptome_results html
extract_matrix html
filter_ctd_genes html
filter_genes_without_1to1_homolog html
filter_nonorthologs html
filter_variance_quantiles html
fix_bad_hgnc_symbols html
fix_bad_mgi_symbols html
fix_celltype_names html
fix_celltype_names_full_results html
generate_bootstrap_plots html
generate_bootstrap_plots_for_transcriptome
html
generate_celltype_data html
generate_controlled_bootstrap_geneset html
get_celltype_table html
get_ctd_levels html
get_exp_data_for_bootstrapped_genes html
get_graph_theme html
get_sig_results html
get_summed_proportions html
is_32bit html
is_celltypedataset html
is_ctd_standardised html
is_delayed_array html
is_matrix html
is_sparse_matrix html
list_species html
load_rdata html
max_ctd_depth html
merge_ctd html
merge_sce html
merge_sce_list html
merge_two_expfiles html
merged_ewce html
message_parallel html
messager html
myScalesComma html
plot_bootstrap_plots html
plot_ctd html
plot_log_bootstrap_distributions html
plot_with_bootstrap_distributions html
prep.dendro html
prep_dendro html
prepare_genesize_control_network html
prepare_tt html
report_dge html
report_results html
run_deseq2 html
run_limma html
run_mast html
sce_lists_apply html
sce_merged_apply html
sct_normalize html
standardise_ctd html
to_dataframe html
to_delayed_array html
to_sparse_matrix html
** 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)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'GeneStructureTools' is missing or broken
Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
DESCRIPTION file of package 'Pviz' is missing or broken
done
EWCE.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 (79reserved).
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 ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpkvBDyg/ctd_testthat.rda
1 core(s) assigned as workers (79reserved).
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 ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpkvBDyg/ctd_testthat.rda
snapshotDate(): 2022-03-16
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 core(s) assigned as workers (79reserved).
Converting to sparse matrix.
Converting to sparse matrix.
1 core(s) assigned as workers (79reserved).
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 42.8722 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 (79reserved).
Generating gene background for mouse x human ==> human
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.
--
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.
--
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
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.
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
Converting to sparse matrix.
Converting to sparse matrix.
Checking gene list inputs.
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.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
17 hit genes remain after filtering.
Computing summed proportions.
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 2.247814 4.046487 0
Loading required namespace: cowplot
Generating gene background for mouse x human ==> human
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.
--
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.
--
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
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.
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.
Converting to sparse matrix.
Converting to sparse matrix.
Aligning celltype names with standardise_ctd format.
Generating bootstrap plot: microglia
Warning: genelistSpecies not provided. Setting to 'human' 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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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
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.
--
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.
--
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
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.
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.
Using intersect between background gene lists: 16,482 genes.
Standardising sct_data.
Converting to sparse matrix.
Converting to sparse matrix.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (79reserved).
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.
Standardising CellTypeDataset
Checking gene list inputs.
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.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
6 hit genes remain after filtering.
Computing summed proportions.
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 endothelial_mural 1 0 1.963288 9.297121 0
2 microglia 1 0 2.194689 2.554997 0
1 core(s) assigned as workers (79reserved).
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.
Standardising CellTypeDataset
Checking gene list inputs.
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.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
5 hit genes remain after filtering.
Computing summed proportions.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
3 significant cell type enrichment results @ q<0.05 :
CellType annotLevel p fold_change sd_from_mean q
1 pyramidal_SS 1 0 2.259588 4.064393 0
2 interneurons 1 0 1.902251 2.589733 0
3 pyramidal_CA1 1 0 1.422274 1.418130 0
Warning: genelistSpecies not provided. Setting to 'human' 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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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
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.
--
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.
--
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
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.
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.
Using intersect between background gene lists: 16,482 genes.
Standardising sct_data.
Converting to sparse matrix.
Converting to sparse matrix.
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.
microglia : Saving bootstrap plot.
oligodendrocytes : Saving bootstrap plot.
astrocytes_ependymal : Saving bootstrap plot.
interneurons : Saving bootstrap plot.
pyramidal_SS : Saving bootstrap plot.
pyramidal_CA1 : Saving bootstrap plot.
Generating exp data for bootstrap genes.
Converting data for bootstrap tests to sparse matrices.
pyramidal_SS : Saving bootstrap plot.
interneurons : Saving bootstrap plot.
pyramidal_CA1 : Saving bootstrap plot.
oligodendrocytes : Saving bootstrap plot.
astrocytes_ependymal : Saving bootstrap plot.
microglia : Saving bootstrap plot.
endothelial_mural : Saving bootstrap plot.
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 (79reserved).
1 core(s) assigned as workers (79reserved).
Generating gene background for mouse x human ==> human
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.
--
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.
--
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
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.
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
Converting to sparse matrix.
Converting to sparse matrix.
Checking gene list inputs.
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.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running with gene size control.
Warning: genelistSpecies not provided. Setting to 'human' 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 61,450 rows retrieved.
Returning all 61,450 genes from human.
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 61,450 rows retrieved.
Returning all 61,450 genes from human.
61,450 human Ensembl IDs and 39,584 human Gene Symbols imported.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Controlled bootstrapping network generated.
20 hit genes remain after filtering.
Computing summed proportions.
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 3.216142 6.667824 0
2 astrocytes_ependymal 1 0 2.415910 3.655548 0
1 core(s) assigned as workers (79reserved).
Returning 15,604 unique genes from the user-supplied bg.
Standardising CellTypeDataset
Converting to sparse matrix.
Converting to sparse matrix.
Checking gene list inputs.
Returning 15,604 unique genes from the user-supplied bg.
Standardising sct_data.
Converting gene list input to standardised human genes.
1 core(s) assigned as workers (79reserved).
Returning 15,589 unique genes from the user-supplied bg.
Standardising CellTypeDataset
Converting to sparse matrix.
Converting to sparse matrix.
Checking gene list inputs.
Returning 15,589 unique genes from the user-supplied bg.
Standardising sct_data.
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.
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 (79reserved).
Generating gene background for mouse x rat ==> human
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.
--
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.
--
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
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.
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.
--
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.
--
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.
Dropping 607 genes that have multiple ortholog_gene per input_gene.
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
Converting to sparse matrix.
Converting to sparse matrix.
Checking gene list inputs.
Returning 15,450 unique genes from the user-supplied bg.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
15 hit genes remain after filtering.
Computing summed proportions.
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 2.157897 4.970799 0
Standardising CellTypeDataset
Level: 1
Converting to sparse matrix.
Level: 2
Converting to sparse matrix.
1 core(s) assigned as workers (79reserved).
Generating gene background for monkey x mouse ==> human
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.
--
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.
--
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 203 genes that have multiple input_gene per ortholog_gene.
Dropping 221 genes that have multiple ortholog_gene per input_gene.
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 :
1,730 / 16,816 (10%)
Total genes remaining after convert_orthologs :
15,086 / 16,816 (90%)
--
=========== REPORT SUMMARY ===========
15,075 / 16,816 (89.65%) target_species genes remain after ortholog conversion.
15,075 / 19,129 (78.81%) reference_species genes remain after ortholog conversion.
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.
--
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.
--
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
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.
13,873 intersect background genes used.
Standardising CellTypeDataset
Converting to sparse matrix.
Converting to sparse matrix.
Checking gene list inputs.
Returning 13,873 unique genes from the user-supplied bg.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
0 hit genes remain after filtering.
Computing summed proportions.
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 (79reserved).
Generating gene background for godzilla x mouse ==> human
1 core(s) assigned as workers (79reserved).
Generating gene background for mouse x human ==> human
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.
--
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.
--
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
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.
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
Converting to sparse matrix.
Converting to sparse matrix.
Checking gene list inputs.
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.
Standardising sct_data.
Converting gene list input to standardised human genes.
1 core(s) assigned as workers (79reserved).
Returning 15,604 unique genes from the user-supplied bg.
Standardising CellTypeDataset
Converting to sparse matrix.
Converting to sparse matrix.
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.
1 core(s) assigned as workers (79reserved).
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 0.9998851 secs
1 core(s) assigned as workers (79reserved).
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 ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpkvBDyg/ctd_kiCortexOnly.rda
1 core(s) assigned as workers (79reserved).
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 ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpkvBDyg/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
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
Level: 1
Converting to sparse matrix.
Level: 2
Converting to sparse matrix.
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.
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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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
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.
--
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.
--
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
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.
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.
Using intersect between background gene lists: 16,482 genes.
Standardising sct_data.
Converting to sparse matrix.
Converting to sparse matrix.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (79reserved).
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.
Standardising CellTypeDataset
Checking gene list inputs.
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.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
28 hit genes remain after filtering.
Computing summed proportions.
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 1.527961 4.832718 0
1 core(s) assigned as workers (79reserved).
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.
Standardising CellTypeDataset
Checking gene list inputs.
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.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
27 hit genes remain after filtering.
Computing summed proportions.
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.
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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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
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.
--
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.
--
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
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.
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.
Using intersect between background gene lists: 16,482 genes.
Standardising sct_data.
Converting to sparse matrix.
Converting to sparse matrix.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (79reserved).
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.
Standardising CellTypeDataset
Checking gene list inputs.
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.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
10 hit genes remain after filtering.
Computing summed proportions.
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 1.61466 2.093933 0
1 core(s) assigned as workers (79reserved).
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.
Standardising CellTypeDataset
Checking gene list inputs.
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.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
8 hit genes remain after filtering.
Computing summed proportions.
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 1.514637 2.263177 0
Warning: genelistSpecies not provided. Setting to 'human' 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.
Dropping 56 genes that have multiple ortholog_gene per input_gene.
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
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.
--
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.
--
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.
Dropping 498 genes that have multiple ortholog_gene per input_gene.
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.
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.
Using intersect between background gene lists: 16,482 genes.
Standardising sct_data.
Converting to sparse matrix.
Converting to sparse matrix.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (79reserved).
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.
Standardising CellTypeDataset
Checking gene list inputs.
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.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
11 hit genes remain after filtering.
Computing summed proportions.
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 oligodendrocytes 1 0 1.567759 2.092819 0
1 core(s) assigned as workers (79reserved).
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.
Standardising CellTypeDataset
Checking gene list inputs.
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.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
9 hit genes remain after filtering.
Computing summed proportions.
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
trying URL 'http://www.informatics.jax.org/downloads/reports/MRK_List2.rpt'
length 38876508 bytes (37.1 MB)
==================================================
downloaded 37.1 MB
Check 1000Check 3005
1 core(s) assigned as workers (79reserved).
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 0.734283 secs
1 core(s) assigned as workers (79reserved).
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 ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpkvBDyg/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
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 rows do not have proper MGI symbols
Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 rows do not have proper MGI symbols
Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 rows do not have proper MGI symbols
Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
10 of 10 are not proper HGNC symbols.
Possible corruption of gene names by excel: Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
10 of 10 are not proper HGNC symbols.
Possible corruption of gene names by excel: Mar-01
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
10 of 10 are not proper HGNC symbols.
Possible corruption of gene names by excel: Mar-01
Maps last updated on: Thu Oct 24 12:31:05 2019
Maps last updated on: Thu Oct 24 12:31:05 2019
9 of 10 gene symbols corrected.
1 of 10 gene symbols cannot be mapped.
Converting to sparse matrix.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 rows do not have proper MGI symbols
Tm4sf12
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 poorly annotated genes are replicates of existing genes. These are:
Tspan12
Converting to sparse matrix.
1 rows should have been corrected by checking synonyms.
0 rows STILL do not have proper MGI symbols.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
0 rows do not have proper MGI symbols
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
669 rows do not have proper MGI symbols
2310042E22Rik, BC005764, C130030K03Rik, Stmn1-rs1, Gm9846, E130309F12Rik, Fam211b, AI848285, Acpl2, 9630033F20Rik, Adrbk2, Syne1_loc2, Adc, Dlx1os, LOC106740, Pdxp, Atp6v0c-ps2, 2900056M20Rik, Epb4.1l1, A330050F15Rik
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
308 rows do not have proper MGI symbols
2310042E22Rik, BC005764, C130030K03Rik, Stmn1-rs1, Gm9846, E130309F12Rik, Fam211b, AI848285, Acpl2, 9630033F20Rik, Adrbk2, Syne1_loc2, Adc, Dlx1os, LOC106740, Pdxp, Atp6v0c-ps2, 2900056M20Rik, Epb4.1l1, A330050F15Rik
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 poorly annotated genes are replicates of existing genes. These are:
Hjurp
Converting to sparse matrix.
185 rows should have been corrected by checking synonyms.
126 rows STILL do not have proper MGI symbols.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
308 rows do not have proper MGI symbols
2310042E22Rik, BC005764, C130030K03Rik, Stmn1-rs1, Gm9846, E130309F12Rik, Fam211b, AI848285, Acpl2, 9630033F20Rik, Adrbk2, Syne1_loc2, Adc, Dlx1os, LOC106740, Pdxp, Atp6v0c-ps2, 2900056M20Rik, Epb4.1l1, A330050F15Rik
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 poorly annotated genes are replicates of existing genes. These are:
Hjurp
Converting to sparse matrix.
185 rows should have been corrected by checking synonyms.
126 rows STILL do not have proper MGI symbols.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 core(s) assigned as workers (79reserved).
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.
=========== 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 ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpkvBDyg/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.
N remaining at each quantile filter:
>=0 >=1 >=2 >=3 >=4 >=5 >=6 >=7 >=8 >=9 >=10
300 155 99 77 60 54 46 41 40 38 36
246 / 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 5.671124 secs
Computing corrected UMI count matrix
|
| | 0%
|
|======================================================================| 100%
Filtering by variance quantiles.
Converting to DelayedArray.
N remaining at each quantile filter:
>=0
300
300 / 300 genes dropped @ DGE min_variance_quantile >= 5
Filtering by variance quantiles.
Converting to DelayedArray.
N remaining at each quantile filter:
>=0 >=1 >=2 >=3 >=4 >=5 >=6 >=7 >=8 >=9 >=10
300 293 284 273 263 255 247 237 229 224 218
45 / 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
N remaining at each quantile filter:
>=0 >=1 >=2 >=3 >=4 >=5 >=6 >=7 >=8 >=9 >=10
300 273 253 231 218 209 194 181 174 161 152
91 / 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
Converting level: level_2
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
Converting level: level_2
ctd2
+ CTD ==> SingleCellExperiment
Converting level: level_1
Converting level: level_2
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 ==> D:\biocbuild\bbs-3.15-bioc\tmpdir\RtmpkvBDyg/merged/CTD_SCE_merged.union.rds
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
0 non-overlapping gene(s) removed from exp1.
0 non-overlapping gene(s) removed from exp2.
19,972 intersecting genes remain.
Converting to data.frame
Converting to data.frame
Converting to sparse matrix.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
DGE:: Limma...
Loading required namespace: DESeq2
DGE:: DESeq2...
1 core(s) assigned as workers (79reserved).
converting counts to integer mode
Note: levels of factors in the design contain characters other than
letters, numbers, '_' and '.'. It is recommended (but not required) to use
only letters, numbers, and delimiters '_' or '.', as these are safe characters
for column names in R. [This is a message, not a warning or an error]
estimating size factors
Note: levels of factors in the design contain characters other than
letters, numbers, '_' and '.'. It is recommended (but not required) to use
only letters, numbers, and delimiters '_' or '.', as these are safe characters
for column names in R. [This is a message, not a warning or an error]
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
-- note: fitType='parametric', but the dispersion trend was not well captured by the
function: y = a/x + b, and a local regression fit was automatically substituted.
specify fitType='local' or 'mean' to avoid this message next time.
Note: levels of factors in the design contain characters other than
letters, numbers, '_' and '.'. It is recommended (but not required) to use
only letters, numbers, and delimiters '_' or '.', as these are safe characters
for column names in R. [This is a message, not a warning or an error]
final dispersion estimates
Note: levels of factors in the design contain characters other than
letters, numbers, '_' and '.'. It is recommended (but not required) to use
only letters, numbers, and delimiters '_' or '.', as these are safe characters
for column names in R. [This is a message, not a warning or an error]
fitting model and testing
Note: levels of factors in the design contain characters other than
letters, numbers, '_' and '.'. It is recommended (but not required) to use
only letters, numbers, and delimiters '_' or '.', as these are safe characters
for column names in R. [This is a message, not a warning or an error]
Loading required namespace: MAST
`fData` has no primerid. I'll make something up.
`cData` has no wellKey. I'll make something up.
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 107 ]
[ FAIL 0 | WARN 1 | SKIP 0 | PASS 107 ]
>
> proc.time()
user system elapsed
366.39 56.23 447.64
EWCE.Rcheck/EWCE-Ex.timings
| name | user | system | elapsed | |
| add_res_to_merging_list | 7.18 | 1.53 | 9.94 | |
| bin_columns_into_quantiles | 3.85 | 0.24 | 4.38 | |
| bin_specificity_into_quantiles | 4.59 | 0.33 | 5.11 | |
| bootstrap_enrichment_test | 10.58 | 0.65 | 11.56 | |
| check_ewce_genelist_inputs | 9.83 | 0.77 | 11.16 | |
| check_percent_hits | 0 | 0 | 0 | |
| controlled_geneset_enrichment | 13.87 | 1.65 | 16.56 | |
| ctd_to_sce | 3.57 | 0.18 | 4.00 | |
| drop_uninformative_genes | 2.57 | 0.47 | 3.24 | |
| ewce_expression_data | 9.97 | 0.82 | 11.15 | |
| ewce_plot | 0.21 | 0.02 | 0.22 | |
| example_bootstrap_results | 0 | 0 | 0 | |
| example_transcriptome_results | 0 | 0 | 0 | |
| filter_genes_without_1to1_homolog | 13.51 | 0.79 | 14.61 | |
| filter_nonorthologs | 14.03 | 0.57 | 14.98 | |
| fix_bad_hgnc_symbols | 0.85 | 0.21 | 1.34 | |
| fix_bad_mgi_symbols | 4.76 | 0.75 | 6.05 | |
| fix_celltype_names | 0 | 0 | 0 | |
| generate_bootstrap_plots | 11.13 | 1.03 | 12.49 | |
| generate_bootstrap_plots_for_transcriptome | 14.46 | 0.83 | 15.78 | |
| generate_celltype_data | 3.48 | 0.40 | 4.17 | |
| get_celltype_table | 2.81 | 0.53 | 3.52 | |
| list_species | 0.01 | 0.00 | 0.01 | |
| load_rdata | 0 | 0 | 0 | |
| merge_ctd | 10.79 | 0.91 | 11.85 | |
| merge_sce | 4.98 | 0.28 | 5.57 | |
| merge_two_expfiles | 3.00 | 0.56 | 3.75 | |
| merged_ewce | 20.76 | 1.32 | 22.66 | |
| plot_ctd | 3.86 | 0.26 | 4.42 | |
| sct_normalize | 10.84 | 0.63 | 11.64 | |
| standardise_ctd | 6.10 | 0.37 | 6.77 | |