FastSEAscore: Calculate the enrichment score of the pathways .
In ssMutPA: Single-Sample Mutation-Based Pathway Analysis

FastSEAscore

R Documentation

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)

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.

Value

Enrichment scores of pathways based on predefined gene ranked lists.

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]

ssMutPA documentation built on Oct. 16, 2024, 1:06 a.m.