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 1.2.4 Index]