gsea2 {corto}R Documentation

2-way GSEA GSEA Gene set enrichment analysis of two complementary gene sets using gsea

Description

2-way GSEA GSEA Gene set enrichment analysis of two complementary gene sets using gsea

Usage

gsea2(
  reflist,
  set1,
  set2,
  method = c("permutation", "pareto"),
  np = 1000,
  w = 1,
  gsea_null = NULL
)

Arguments

reflist

named vector of reference scores

set1

element set 1

set2

element set 1

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 list of 2 GSEA objects. Each of which is a list of 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))
set1<-paste0('gene',sample(1:200,50))
set2<-paste0('gene',sample(801:1000,50))
obj<-gsea2(reflist,set1,set2,method='pareto',np=1000)
obj$p.value

[Package corto version 1.1.6 Index]