callGSVA: GSVA enrichment analysis
In SISPA: SISPA: Method for Sample Integrated Set Profile Analysis

Description Usage Arguments Details Value See Also Examples

View source: R/callGSVA.R

Estimates GSVA enrichment zscores.

1	callGSVA(x,y)

`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

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

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

GSVA

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)