gsea: GSEA

In federicogiorgi/vulcan: VirtUaL ChIP-Seq data Analysis using Networks

Description

This function performs Gene Set Enrichment Analysis

Usage

gsea(reflist, set, method = c("permutation", "pareto"), np = 1000, w = 1,
  gsea_null = NULL)

Arguments

reflist	named vector of reference scores
set	element set
method	one of 'permutation' or 'pareto'
np	Number of permutations (Default: 1000)
w	exponent used to raise the supplied scores. Default is 1 (original scores unchanged)
gsea_null	a GSEA null distribution (Optional)

Value

A GSEA object. Basically a list of s components:

ES

The enrichment score

NES

The normalized enrichment socre

ledge

The items in the leading edge

p.value

The permutation-based p-value

Examples

reflist<-setNames(-sort(rnorm(1000)),paste0('gene',1:1000))
set<-paste0('gene',sample(1:200,50))
obj<-gsea(reflist,set,method='pareto',np=1000)
obj$p.value

federicogiorgi/vulcan documentation built on May 27, 2019, 7:25 a.m.