GSA.listsets: List the results from a Gene set analysis

In GSA: Gene Set Analysis

List the results from a Gene set analysis

Description

List the results from a call to GSA (Gene set analysis)

Usage

GSA.listsets(GSA.obj, geneset.names = NULL, maxchar = 20, FDRcut = 0.2)

Arguments

GSA.obj

Object returned by GSA function

.

geneset.names	Optional vector of names for the gene sets
maxchar	Maximum number of characters in printed output
FDRcut	False discovery rate cutpoint for listed sets. A value of 1 will cause all sets to be listed

.

Details

This function list the sigificant gene sets, based on a call to the GSA (Gene set analysis) function.

Value

A list with components

FDRcut	The false discovery rate threshold used.
negative	A table of the negative gene sets. "Negative" means that lower expression of most genes in the gene set correlates with higher values of the phenotype y. Eg for two classes coded 1,2, lower expression correlates with class 2. For survival data, lower expression correlates with higher risk, i.e shorter survival (Be careful, this can be confusing!)
positive	A table of the positive gene sets. "Positive" means that higher expression of most genes in the gene set correlates with higher values of the phenotype y. See "negative" above for more info.
nsets.neg	Number of negative gene sets
nsets.pos	Number of positive gene sets

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 radnom 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)


GSA.listsets(GSA.obj, geneset.names=geneset.names,FDRcut=.5)

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