ssMutPA (version 0.1.2)

FastSEAscore: Calculate the enrichment score of the pathways .

Description

The function `FastSEAscore` is used to calculate the pathway enrichment score.

Usage

FastSEAscore(labels.list, correl_vector)

Value

Enrichment scores of pathways based on predefined gene ranked lists.

Arguments

labels.list

The position of the genes in the pathway in the ranked gene list .

correl_vector

A ranked list of all genes in the PPI network.

Examples

#load the data
pathway_path<-system.file("extdata","kegg_323_gmt.Rdata",package = "ssMutPA")
load(pathway_path)
pathway_list<-split(kegg_323_gmt[,2],kegg_323_gmt[,1])
data(RWR_res)
gene_list<-sort(RWR_res,decreasing=TRUE)
tag.indicator <- sign(match(names(gene_list), pathway_list[[1]], nomatch = 0))
#perform the function `FastSEAscore`.
Path_ES<-FastSEAscore(labels.list=tag.indicator,correl_vector = gene_list)
names(Path_ES)<-names(pathway_list)[1]