Description

runs a functional enrichment analysis with gprofiler2

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]

de_file (file)

CSV or TSV-format tabular file with differential analysis outputs

*.{csv,tsv}

contrast_variable (string)

The contrast variable that is being investigated in DE analysis, e.g. “treatment”.

reference (string)

The contrast level of the reference samples, e.g. “control”

target (string)

The contrast level of the target samples, e.g. “treated”

background_file (file)

Path to a CSV/TSV/TXT file listing gene IDs that should be used as the background (will override count_file). This can be an expression matrix (see also background_column parameter); if so, will only consider those genes with an expression value > 0 in at least one sample. Alternatively, this can be a TXT file containing only a list of gene IDs.

*.{csv,tsv,txt}

gmt_file (file)

Path to a GMT file downloaded from g

that should be queried instead of the online databases

*.gmt

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]

all_enrich (file)

TSV file; table listing all enriched pathways that were found. This table will always be created (empty if no enrichment was found), the other output files are only created if enriched pathways were found

*gprofiler2.*all_enriched_pathways.tsv

rds (file)

RDS file; R object containing the results of the gost query

*gprofiler2.*gost_results.rds

plot_png (file)

PNG file; Manhattan plot of all enriched pathways

*gprofiler2.*gostplot.png

plot_html (file)

HTML file; interactive Manhattan plot of all enriched pathways

*gprofiler2.*gostplot.html

sub_enrich (file)

TSV file; table listing enriched pathways that were found from one particular source

*gprofiler2.*sub_enriched_pathways.tsv

sub_plot (file)

PNG file; bar plot showing the fraction of genes that were found enriched in each pathway

*gprofiler2.*sub_enriched_pathways.png

filtered_gmt (file)

GMT file that was provided as input or that was downloaded from g

if no input GMT file was given; filtered for the selected datasources

*ENSG_filtered.gmt

session_info (file)

Log file containing information about the R session that was run for this module

*R_sessionInfo.log

versions (file)

File containing software versions

versions.yml

Tools

gprofiler2
GPL v2

An R interface corresponding to the 2019 update of g:Profiler web tool.