writeFemap {fedup} | R Documentation

## Writes an enrichment dataset file for use in Cytoscape EnrichmentMap.

### 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)

[Package fedup version 1.2.0 Index]