GSA.plot {GSA} | R Documentation |
Plots the results from a call to GSA (Gene set analysis)
GSA.plot(GSA.obj, fac=1, FDRcut = 1)
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 |
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This function makes a plot of the significant gene sets, based on a call to the GSA (Gene set analysis) function.
Robert Tibshirani
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
######### 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)