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

Description Usage Arguments Details Author(s) References Examples

Description

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

Usage

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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.

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

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######### 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)


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