callGSVA: GSVA enrichment analysis

In BhaktiDwivedi/SISPA: SISPA: Method for Sample Integrated Set Profile Analysis

Description

Estimates GSVA enrichment zscores.

Usage

callGSVA(x,y)

Arguments

x	A data frame or matrix of gene or probe expression values where rows corrospond to genes and columns corrospond to samples
y	A list of genes as data frame or vector

Details

This function uses "zscore" gene-set enrichment method in the estimation of gene-set enrichment scores per sample.

Value

A gene-set by sample matrix of GSVA enrichment zscores.

See Also

GSVA

Examples

g <- 10 ## number of genes
s <- 30 ## number of samples
## sample data matrix with values ranging from 1 to 10
rnames <- paste("g", 1:g, sep="")
cnames <- paste("s", 1:s, sep="")
expr <- matrix(sample.int(10, size = g*s, replace = TRUE), nrow=g, ncol=s, dimnames=list(rnames, cnames))
## genes of interest
genes <- paste("g", 1:g, sep="")
## Estimates GSVA enrichment zscores.
callGSVA(expr,genes)

BhaktiDwivedi/SISPA documentation built on Aug. 31, 2021, 7:41 p.m.