FindPathwayEnrichment: Find Reactome pathways enriched from proximal binding

In rramaker/GRNF: Gene Regulatory Network Finder

Description

Find Reactome pathways enriched from proximal binding

Usage

FindPathwayEnrichment(distanceFrame, geneSet = NULL, minPathwayGenes = 5,
  numCores = 4)

Arguments

distanceFrame	A dataframe resulting from the output of the GeneToPeakDist function. Should have two columns with the first having ENSEMBL gene IDs and the second the distance to the nearest ChIP peak.
geneSet	A character vector of ENSEMBL gene IDs to perform enrichment for proximal binding analysis on. If NULL, pathway analysis on all reactome pathways will be used for analysis. Defaults to NULL.
minPathwayGenes	A numeric indicating the minimum number of genes in a pathway required for inclusion in pathway analysis. Defaults to 5.
numCores	A numeric indicating the number of cores the function can use via R's parallel package. Defaults to 4.

Value

Returns a vector of one-sided Wilcoxon p-values with the alternate hypothesis of pathway genes enriched for shorter distances to the nearest ChIP-peak relative to all non-pathway genes.

Note

Reactome

Terms of Use: http://www.reactome.org/pages/about/license-agreement/

rramaker/GRNF documentation built on May 20, 2019, 2:23 p.m.