Writes an enrichment dataset file for use in Cytoscape EnrichmentMap.

Source: R/femap.R

Writes an enrichment dataset file for use in Cytoscape EnrichmentMap.

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)

#> Running fedup with:
#>  => 2 test set(s)
#>   + FASN_negative: 379 genes
#>   + FASN_positive: 298 genes
#>  => 17804 background genes
#>  => 1437 pathway annotations
#> All done!
# Write out results to temp folder
resultsFolder <- tempdir()
writeFemap(fedupRes, resultsFolder)

#> Wrote out EM-formatted fedup results file to /var/folders/mh/_0z2r5zj3k75yhtgm6l7xy3m0000gn/T//RtmpaRu10f/femap_FASN_negative.txt
#> Wrote out EM-formatted fedup results file to /var/folders/mh/_0z2r5zj3k75yhtgm6l7xy3m0000gn/T//RtmpaRu10f/femap_FASN_positive.txt