# Fisher's Test for Enrichment and Depletion of User-Defined Pathways

## Documentation for package ‘fedup’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

geneDouble | Example list of a background set and two sets of test genes to use for enrichment analysis.
geneMulti | Example list of a background set and multiple sets of test genes to use for enrichment analysis.
geneSingle | Example list of a background set and single set of test genes to use for enrichment analysis.
pathwaysGMT | Named list of human pathway annotations obtained from a GMT file.
pathwaysTXT | Example list of SAFE terms obtained from a TXT file.
pathwaysXLSX | Example list of SAFE terms obtained from a XLSX file.
plotDotPlot | Visualizes fedup enrichment and depletion results using ggplot.
plotFemap | Draws a network representation of overlaps among pathway enrichment results using EnrichmentMap (EM) in Cytoscape.
prepInput | Prepares input gene list for runFedup.
readPathways | Returns a list of pathways from various file formats.
runFedup | Runs pathway enrichment and depletion analysis using a Fisher's exact test.
writeFemap | Writes an enrichment dataset file for use in Cytoscape EnrichmentMap.
writePathways | Writes a set of pathways (list of vectors) to a GMT file.