quickenrichmentscore: quickenrichmentscore

In zhilongjia/PAGE: Gene Expression Signature Similarity based on Parametric Analysis of Gene Set Enrichment

Description

quickenrichmentscore

Usage

quickenrichmentscore(S, S1, List)

Arguments

S	rank of up-regualted genes
S1	rank of down-regulated genes
List	a rank vector

Value

similarity based on averaged GSEA Enrichment score

Author(s)

Yang Cao

Source

http://bioconductor.org/packages/GeneExpressionSignature/

Examples

data(Psoriasis_Etanercept_LogFC)
dat <- apply(-Psoriasis_Etanercept_LogFC, 2, rank)
SignatureLength <- 250

# caculate similarity only for some columns
sim_mat <- matrix(-2, ncol=ncol(dat), nrow=ncol(dat))
for (i in 11:15) {
    for (j in 1:10) {
        sim_mat[j,i] <- (quickenrichmentscore(which(dat[,j]<=SignatureLength), 
        which(dat[,j]>=nrow(dat)-SignatureLength+1), dat[,i]) + 
        quickenrichmentscore(which(dat[,i]<=SignatureLength), 
        which(dat[,i]>=nrow(dat)-SignatureLength+1), dat[,j]) )/2
    }

}

zhilongjia/PAGE documentation built on May 4, 2019, 11:22 p.m.