gsea {vulcan} | R Documentation |
This function performs Gene Set Enrichment Analysis
gsea(reflist, set, method = c("permutation", "pareto"), np = 1000, w = 1, gsea_null = NULL)
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) |
A GSEA object. Basically a list of s components:
The enrichment score
The normalized enrichment socre
The items in the leading edge
The permutation-based p-value
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