gsvaEnrichment: GSVA enrichment data and visualization

In rcastelo/GSVA: Gene Set Variation Analysis for Microarray and RNA-Seq Data

GSVA enrichment data and visualization

Description

Extract and plot enrichment data from GSVA scores.

Usage

## S4 method for signature 'gsvaRanksParam'
gsvaEnrichment(
  param,
  column = 1,
  geneSet = 1,
  plot = c("auto", "base", "ggplot", "no"),
  ...
)

Arguments

param	A gsvaRanksParam object obtained with the method gsvaRanks.
column	The column for which we want to retrieve the enrichment data. This parameter is only available in the gsvaEnrichment() method.
geneSet	Either a positive integer number between 1 and the number of available gene sets in param, or a character string with the name of one of the gene sets available in param.
plot	A character string indicating whether an enrichment plot should be produced using either base R graphics (plot="base") or the ggplot2 package (plot="ggplot"), or not (plot="no"). In the latter case, the enrichment data will be returned. By default plot="auto", which implies that if this method is called from an interactive session, a plot using base R graphics will be produced and, otherwise, the enrichment data is returned.
...	Further arguments passed to the plot() function when the previous parameter plot="base".

Value

When plot="no", this method returns the enrichment data. When plot="ggplot", this method returns a ggplot object. When plot="base" no value is returned.

References

Hänzelmann, S., Castelo, R. and Guinney, J. GSVA: Gene set variation analysis for microarray and RNA-Seq data. BMC Bioinformatics, 14:7, 2013. DOI

Examples

library(GSVA)

p <- 10 ## number of genes
n <- 30 ## number of samples
nGrp1 <- 15 ## number of samples in group 1
nGrp2 <- n - nGrp1 ## number of samples in group 2

## consider three disjoint gene sets
geneSets <- list(gset1=paste0("g", 1:3),
                 gset2=paste0("g", 4:6),
                 gset3=paste0("g", 7:10))

## sample data from a normal distribution with mean 0 and st.dev. 1
y <- matrix(rnorm(n*p), nrow=p, ncol=n,
            dimnames=list(paste("g", 1:p, sep="") , paste("s", 1:n, sep="")))

## genes in set1 are expressed at higher levels in the last 'nGrp1+1' to 'n' samples
y[geneSets$set1, (nGrp1+1):n] <- y[geneSets$set1, (nGrp1+1):n] + 2

## build GSVA parameter object
gsvapar <- gsvaParam(y, geneSets)

## calculate GSVA ranks
gsvarankspar <- gsvaRanks(gsvapar)
gsvarankspar

## by default the enrichment data for the first column and the first
## gene set are retrieved
gsvaEnrichment(gsvarankspar)

rcastelo/GSVA documentation built on Dec. 17, 2024, 4:51 p.m.