R: Plot the results from a Gene set analysis

GSA.plot {GSA} | R Documentation

## 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.

### 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.plot(GSA.obj)

[Package GSA version 1.03 Index]