GSA (version 1.03.1)

GSA.plot: Plot the results from a Gene set analysis

Description

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

Usage

GSA.plot(GSA.obj, fac=1, FDRcut = 1)

Arguments

GSA.obj

Object returned by GSA function

fac

value for jittering points in plot ("factor" in called to jitter()

FDRcut

False discovery rate cutpoint for sets to be plotted. A value of 1 (the default) will cause all sets to be plotted

Details

This function makes a plot of the significant gene sets, based on a call to the GSA (Gene set analysis) function.

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

# NOT RUN {
######### 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.plot(GSA.obj)

# }