writeFemap: Writes an enrichment dataset file for use in Cytoscape...

In rosscm/FEDUP: Fisher's Test for Enrichment and Depletion of User-Defined Pathways

Description

Writes an enrichment dataset file for use in Cytoscape EnrichmentMap.

Usage

writeFemap(results, resultsFolder)

Arguments

results	(list) list with ouput results from runFedup
resultsFolder	(char) name of folder to store result file(s)

Value

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)

Examples

# Load example data
data(geneDouble)
data(pathwaysGMT)
# Run fedup
fedupRes <- runFedup(geneDouble, pathwaysGMT)
# Write out results to temp folder
resultsFolder <- tempdir()
writeFemap(fedupRes, resultsFolder)

rosscm/FEDUP documentation built on July 15, 2021, 2:18 a.m.