GSA.genescores: Individual gene scores from a gene set analysis

In GSA: Gene Set Analysis

Individual gene scores from a gene set analysis

Description

Compute individual gene scores from a gene set analysis

Usage

GSA.genescores(geneset.number, genesets,  GSA.obj,  genenames, negfirst=FALSE)

Arguments

geneset.number	Number indicating which gene set is to examined
genesets	The gene set collection
GSA.obj	Object returned by function GSA
genenames	Vector of gene names for gene in expression dataset
negfirst	Should negative genes be listed first? Default FALSE

Details

Compute individual gene scores from a gene set analysis. Useful for looking “inside” a gene set that has been called significant by GSA.

Value

A list with components

res	Matrix of gene names and gene scores (eg t-statistics) for each gene in the gene set

,

Author(s)

Robert Tibshirani

References

Efron, B. and Tibshirani, R. On testing the significance of sets of genes. Stanford tech report rep 2006. http://www-stat.stanford.edu/~tibs/ftp/GSA.pdf

Examples

######### two class unpaired comparison
# y must take values 1,2

set.seed(100)
x<-matrix(rnorm(1000*20),ncol=20)
dd<-sample(1:1000,size=100)

u<-matrix(2*rnorm(100),ncol=10,nrow=100)
x[dd,11:20]<-x[dd,11:20]+u
y<-c(rep(1,10),rep(2,10))


genenames=paste("g",1:1000,sep="")

#create some random gene sets
genesets=vector("list",50)
for(i in 1:50){
 genesets[[i]]=paste("g",sample(1:1000,size=30),sep="")
}
geneset.names=paste("set",as.character(1:50),sep="")

GSA.obj<-GSA(x,y, genenames=genenames, genesets=genesets,
             resp.type="Two class unpaired", nperms=100)

# look at 10th gene set

GSA.genescores(10, genesets, GSA.obj, genenames)

GSA documentation built on May 29, 2024, 7:23 a.m.