writeFemap {fedup} | R Documentation |
Writes an enrichment dataset file for use in Cytoscape EnrichmentMap.
writeFemap(results, resultsFolder)
results |
(list) list with ouput results from runFedup |
resultsFolder |
(char) name of folder to store result file(s) |
Table of pathway enrichment and depletion results formatted as a 'Generic results file'. Rows represent tested pathways. Columns represent:
pathway – pathway ID (must match pathway IDs in the GMT file provided to plotFemap;
description – pathway name or description;
pvalue – enrichment pvalue;
qvalue – BH-corrected pvalue;
status – +1 or -1, to identify enriched or depleted pathways (+1 maps to red, -1 maps to blue)
# Load example data data(geneDouble) data(pathwaysGMT) # Run fedup fedupRes <- runFedup(geneDouble, pathwaysGMT) # Write out results to temp folder resultsFolder <- tempdir() writeFemap(fedupRes, resultsFolder)