computeFDRmedian: computes False Discovery Rate (FDR) taking the median of the...

In galder-max/GSEAlite: GSEA lite performs simple GSEA analysis with few useful functions

Description

computes FDR from scores and permutation scores

Usage

computeFDR(r)

Arguments

r	result list from GSEA analysis with r0 scores; rR random scores

Details

computes FDR from scores and permutation scores

Value

returns a list with two dataframes; one for Up regulation and one for Down regulation

Author(s)

[e-mail]

Examples

     ##creates matrix of expression with rownames = gene names
     m<-matrix(rnorm(10*10000),10000,10)
     rownames(m)<-paste("r",1:10000)    
     
     ## creates list of 10 genesets of size 100
     lG<-lapply(1:10,function(x) paste("r",sample(1:10000,100,rep=F)))
     names(lG)<-paste("GS",1:10)
     
     
     ##performs GSEA analysis
     r<-GSEA.listofgenes(m,lG,nperms=100)

     ##computesFDR for the results
     computeFDRmedian(r)

galder-max/GSEAlite documentation built on Jan. 30, 2021, 10:50 p.m.