samr.pvalues.from.perms {samr} | R Documentation |
Report estimated p-values for each gene, from set of permutations in a SAM analysis
samr.pvalues.from.perms(tt, ttstar)
tt |
Vector of gene scores, returned by samr in component tt |
ttstar |
Matrix of gene scores (p by nperm) from nperm permutations. Returned by samr in component ttstar |
Balasubrimanian Narasimhan and Robert Tibshirani
Taylor, J. and Tibshirani, R. (2005): A tail strength measure for assessing the overall significance in a dataset. Submitted.
#generate some example data 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)) data=list(x=x,y=y, geneid=as.character(1:nrow(x)),genenames=paste("g",as.character(1:nrow(x)),sep=""), logged2=TRUE) samr.obj<-samr(data, resp.type="Two class unpaired", nperms=100) pv=samr.pvalues.from.perms(samr.obj$tt, samr.obj$ttstar)