R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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> library(testthat)
> library(EWCE)
Loading required package: RNOmni
>
> test_check("EWCE")
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Loading required namespace: ggdendro
+ Saving results ==> F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpIbXWtD/ctd_testthat.rda
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpIbXWtD/ctd_testthat.rda
snapshotDate(): 2022-12-16
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
Converting to sparse matrix.
1 core(s) assigned as workers (31 reserved).
Processing block [[1/5, 1/1]] ... OK
Processing block [[2/5, 1/1]] ... OK
Processing block [[3/5, 1/1]] ... OK
Processing block [[4/5, 1/1]] ... OK
Processing block [[5/5, 1/1]] ... OK
Processing block [[1/5, 1/1]] ... OK
Processing block [[2/5, 1/1]] ... OK
Processing block [[3/5, 1/1]] ... OK
Processing block [[4/5, 1/1]] ... OK
Processing block [[5/5, 1/1]] ... OK
Loading required namespace: sctransform
Converting to sparse matrix.
Calculating cell attributes from input UMI matrix: log_umi
Variance stabilizing transformation of count matrix of size 17757 by 3005
Model formula is y ~ log_umi
Get Negative Binomial regression parameters per gene
Using 2000 genes, 3005 cells
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Found 12 outliers - those will be ignored in fitting/regularization step
Second step: Get residuals using fitted parameters for 17757 genes
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Calculating gene attributes
Wall clock passed: Time difference of 46.31366 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 (31 reserved).
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 (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.
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.
Returning 16,482 unique genes from the user-supplied bg.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
17 hit genes remain after filtering.
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
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 (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.
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
Generating bootstrap plot: astrocytes_ependymal
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 (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
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 (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.
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.
Converting to sparse matrix.
Converting to sparse matrix.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Returning 16,482 unique genes from the user-supplied bg.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
6 hit genes remain after filtering.
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 1.884819 4.092025 0
2 microglia 1 0 2.492816 3.122445 0
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Returning 16,482 unique genes from the user-supplied bg.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
5 hit genes remain after filtering.
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 1.837327 4.060324 0
2 pyramidal_SS 1 0 1.880474 2.861583 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 (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
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 (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.
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.
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.
interneurons : Saving bootstrap plot.
oligodendrocytes : Saving bootstrap plot.
astrocytes_ependymal : Saving bootstrap plot.
pyramidal_CA1 : Saving bootstrap plot.
pyramidal_SS : Saving bootstrap plot.
Generating exp data for bootstrap genes.
Converting data for bootstrap tests to sparse matrices.
interneurons : Saving bootstrap plot.
pyramidal_SS : Saving bootstrap plot.
pyramidal_CA1 : Saving bootstrap plot.
oligodendrocytes : Saving bootstrap plot.
microglia : Saving bootstrap plot.
astrocytes_ependymal : 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 (31 reserved).
1 core(s) assigned as workers (31 reserved).
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 (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.
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.
Returning 16,482 unique genes from the user-supplied bg.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running with gene size control.
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 61,769 rows retrieved.
Returning all 61,769 genes from human.
61,769 human Ensembl IDs and 40,153 human Gene Symbols imported.
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Controlled bootstrapping network generated.
17 hit genes remain after filtering.
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 2.01616 3.758104 0
1 core(s) assigned as workers (31 reserved).
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 (31 reserved).
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 (many:1).
Filtering gene_df with gene_map
Returning gene_map as dictionary
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
7 / 22 (32%)
Total genes remaining after convert_orthologs :
15 / 22 (68%)
1 core(s) assigned as workers (31 reserved).
Generating gene background for mouse x rat ==> human
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 (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.
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 (many:1).
Dropping 607 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,813 / 20,616 (23%)
Total genes remaining after convert_orthologs :
15,803 / 20,616 (77%)
--
=========== REPORT SUMMARY ===========
15,803 / 20,616 (76.65%) target_species genes remain after ortholog conversion.
15,803 / 19,129 (82.61%) reference_species genes remain after ortholog conversion.
15,450 intersect background genes used.
Standardising CellTypeDataset
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.
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 2.188004 4.229286 0
Standardising CellTypeDataset
Found 5 matrix types across 2 CTD levels.
Processing level: 1
Converting to sparse matrix.
Processing level: 2
Converting to sparse matrix.
1 core(s) assigned as workers (31 reserved).
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 (many:1).
Dropping 221 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
1,730 / 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 (many:1).
Dropping 498 genes that have multiple ortholog_gene per input_gene (1:many).
Filtering gene_df with gene_map
Adding input_gene col to gene_df.
Adding ortholog_gene col to gene_df.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
4,725 / 21,207 (22%)
Total genes remaining after convert_orthologs :
16,482 / 21,207 (78%)
--
=========== REPORT SUMMARY ===========
16,482 / 21,207 (77.72%) target_species genes remain after ortholog conversion.
16,482 / 19,129 (86.16%) reference_species genes remain after ortholog conversion.
13,873 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.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
0 significant cell type enrichment results @ q<0.05 :
1 core(s) assigned as workers (31 reserved).
Generating gene background for godzilla x mouse ==> human
1 core(s) assigned as workers (31 reserved).
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 (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.
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.
Returning 16,482 unique genes from the user-supplied bg.
Standardising sct_data.
Converting gene list input to standardised human genes.
1 core(s) assigned as workers (31 reserved).
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 (31 reserved).
Converting to sparse matrix.
Checking for non-expressed genes.
Checking for cells with no expressed genes.
DGE:: Limma...
248 / 1,000 genes dropped @ DGE adj_pval_thresh < 1e-05
Time difference of 0.714035 secs
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpIbXWtD/ctd_kiCortexOnly.rda
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpIbXWtD/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
Found 5 matrix types across 2 CTD levels.
Processing level: 1
Converting to sparse matrix.
Processing 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 (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
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 (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.
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.
Converting to sparse matrix.
Converting to sparse matrix.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Returning 16,482 unique genes from the user-supplied bg.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
28 hit genes remain after filtering.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
1 significant cell type enrichment results @ q<0.05 :
CellType annotLevel p fold_change sd_from_mean q
1 endothelial_mural 1 0 1.628635 4.684982 0
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Returning 16,482 unique genes from the user-supplied bg.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
26 hit genes remain after filtering.
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 1.341278 3.850814 0
2 pyramidal_CA1 1 0 1.214856 2.192119 0
3 interneurons 1 0 1.144435 1.745605 0
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 (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
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 (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.
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.
Converting to sparse matrix.
Converting to sparse matrix.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Returning 16,482 unique genes from the user-supplied bg.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
10 hit genes remain after filtering.
Testing for enrichment in 7 cell types...
Sorting results by p-value.
Computing BH-corrected q-values.
0 significant cell type enrichment results @ q<0.05 :
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Returning 16,482 unique genes from the user-supplied bg.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
8 hit genes remain after filtering.
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 :
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 (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
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 (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.
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.
Converting to sparse matrix.
Converting to sparse matrix.
Using 1st column of tt as gene column: HGNC.symbol
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Returning 16,482 unique genes from the user-supplied bg.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
11 hit genes remain after filtering.
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 1.680834 3.07176 0
1 core(s) assigned as workers (31 reserved).
Standardising CellTypeDataset
Checking gene list inputs.
Returning 16,482 unique genes from the user-supplied bg.
Standardising sct_data.
Converting gene list input to standardised human genes.
Running without gene size control.
9 hit genes remain after filtering.
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
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
Converting to sparse matrix.
Processing level: 2
Converting to sparse matrix.
Filtering CTD to 100 genes.
level: level_1
Found 5 matrix types across 1 CTD levels.
- mean_exp
- median_exp
- specificity
- median_specificity
- specificity_quantiles
level: level_2
Found 5 matrix types across 1 CTD levels.
- mean_exp
- median_exp
- specificity
- median_specificity
- specificity_quantiles
see ?ewceData and browseVignettes('ewceData') for documentation
loading from cache
Check 1000Check 3005
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
Checking for non-expressed genes.
Checking for cells with no expressed genes.
DGE:: Limma...
248 / 1,000 genes dropped @ DGE adj_pval_thresh < 1e-05
Time difference of 0.7384312 secs
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpIbXWtD/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 83877092 bytes (80.0 MB)
==================================================
downloaded 80.0 MB
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 (31 reserved).
Preparing gene_df.
Dense matrix format detected.
Extracting genes from rownames.
100 genes extracted.
Converting mouse ==> human orthologs using: homologene
Retrieving all organisms available in homologene.
Mapping species name: mouse
Common name mapping found for mouse
1 organism identified from search: 10090
Retrieving all organisms available in homologene.
Mapping species name: human
Common name mapping found for human
1 organism identified from search: 9606
Checking for genes without orthologs in human.
Extracting genes from input_gene.
91 genes extracted.
Extracting genes from ortholog_gene.
91 genes extracted.
Checking for genes without 1:1 orthologs.
Filtering gene_df with gene_map
Setting ortholog_gene to rownames.
Converting obj to sparseMatrix.
=========== REPORT SUMMARY ===========
Total genes dropped after convert_orthologs :
9 / 100 (9%)
Total genes remaining after convert_orthologs :
91 / 100 (91%)
Converting to sparse matrix.
Converting to DelayedArray.
+ Calculating normalized mean expression.
Converting to sparse matrix.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpIbXWtD/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 6.601578 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
Returning all possible matrix names.
Converting level: level_2
Returning all possible matrix names.
The assay 'mean_exp' will be used to determine the proportion of zeroes for each batch.
Converting CTD to merged SCEs
ctd1
+ CTD ==> SingleCellExperiment
Converting level: level_1
Returning all possible matrix names.
Converting level: level_2
Returning all possible matrix names.
ctd2
+ CTD ==> SingleCellExperiment
Converting level: level_1
Returning all possible matrix names.
Converting level: level_2
Returning all possible matrix names.
Merging SCE at level: 1
[1] "ctd1"
[1] "15259 x 7"
[1] "ctd2"
[1] "15259 x 7"
The assay 'mean_exp' will be used to determine the proportion of zeroes for each batch.
Merging SCE at level: 2
[1] "ctd1"
[1] "15259 x 48"
[1] "ctd2"
[1] "15259 x 48"
The assay 'mean_exp' will be used to determine the proportion of zeroes for each batch.
[1] "level_1"
[1] "level_2"
Saving SCE_merged ==> F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpIbXWtD/merged/CTD_SCE_merged.union.rds
+ Must set `as_SCE=TRUE` in order to merge CTD.
+ Returning merged CTD.
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpIbXWtD/ctd_file1fb441f13310level_1.rda
+ Returning list of CTD file name, and the CTD itself.
1 core(s) assigned as workers (31 reserved).
Converting to sparse matrix.
+ Calculating normalized mean expression.
Converting to sparse matrix.
+ Calculating normalized specificity.
Converting to sparse matrix.
Converting to sparse matrix.
+ Saving results ==> F:\biocbuild\bbs-3.17-bioc-rtools43\tmpdir\RtmpIbXWtD/ctd_file1fb45a2a6974level_2.rda
+ Returning list of CTD file name, and the CTD itself.
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 (31 reserved).
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 40 | SKIP 0 | PASS 111 ]
[ FAIL 0 | WARN 40 | SKIP 0 | PASS 111 ]
>
> proc.time()
user system elapsed
463.39 23.98 493.14