gsea {corto}R Documentation

GSEA

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

[Package corto version 1.1.6 Index]