modules/gprofiler2_gost
runs a functional enrichment analysis with gprofiler2
Input
Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]
The contrast variable that is being investigated in DE analysis, e.g. “treatment”.
The name of the analyzed organism consisting of the first letter of the genus and the entire species name, e.g. for homo sapiens: hsapiens
Comma-separated list of data sources to search for pathways, e.g. ‘GO,REAC’. Check https://rdrr.io/cran/gprofiler2/man/gost.html for a list of available sources
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}Output
Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]
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.tsvHTML file; interactive Manhattan plot of all enriched pathways
*gprofiler2.*gostplot.htmlTSV file; table listing enriched pathways that were found from one particular source
*gprofiler2.*sub_enriched_pathways.tsvPNG file; bar plot showing the fraction of genes that were found enriched in each pathway
*gprofiler2.*sub_enriched_pathways.pngGMT 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.gmtLog file containing information about the R session that was run for this module
*R_sessionInfo.log