corto (version 1.2.4)

ssgsea: ssGSEA

Description

This function performs single sample GSEA

Usage

ssgsea(inmat, groups, scale = TRUE, minsize = 10)

Value

A matrix of Normalized Enrichment Scores (NES), which can be converted to p-values using the function _corto::z2p_

Arguments

inmat

A numeric matrix, with rownames/rows as genes or features, and colnames/columns as sample names

groups

a named list. Names are names of the groups (e.g. pathways) and elements are character vectors indicating gene or feature names (that should match, at least partially, with the rownames of inmat)

scale

Boolean. Wheter the matrix should be row-scaled.

minsize

Numeric. Include only groups with at least this many elements Default is 10

Examples

# A random matrix
set.seed(1)
inmat<-matrix(rnorm(200*50),nrow=200,ncol=50)
rownames(inmat)<-paste0("gene",1:nrow(inmat))
# A random list of groups
groups<-list()
for(i in 1:10){
    somegenes<-sample(rownames(inmat),30)
    groups[[paste0("pathway_",i)]]<-somegenes
}
# Run ssGSEA
nesmat<-ssgsea(inmat,groups)