Hi, Try this: (Used the old data folder)
Compares the spec counts of sub directory with each other. directory<- "/home/arunksa111/dados" GetFileList <- function(directory,number){ setwd(directory) filelist1<-dir()[file.info(dir())$isdir] direct<-dir(directory,pattern = paste("MSMS_",number,"PepInfo.txt",sep=""), full.names = FALSE, recursive = TRUE) direct<-lapply(direct,function(x) paste(directory,"/",x,sep="")) lista<-unlist(direct) output<- list(filelist1,lista) return(output) } ReadDir<-function(FacGroup){ list.new<-lista[FacGroup!=0] read.list<-lapply(list.new, function(x) read.table(x,header=TRUE, sep = "\t")) names(read.list)<-file.list.names[FacGroup!=0] return (read.list) } file.list.names<-GetFileList(directory,23) [[1]] lista<-GetFileList(directory,23) [[2]] FacGroup<-c(1,1,0,2,2,0,0) ListFacGroup<-ReadDir(FacGroup) lst1<-lapply(ListFacGroup,function(x) {x<-within(x,{spec<- as.character(spec)}); x1<- x[x$FDR<0.01,c("Seq","Mod","z","spec")]; x1$counts<-sapply(x1$spec,function(x2) length(unlist(strsplit(x2,","))));x1}) lst2<-lapply(as.data.frame(combn(names(lst1),2),stringsAsFactors=FALSE),function(x) { x1<-merge(lst1[[x[1]]],lst1[[x[2]]],by=c("Seq","Mod","z"));names(x1)[c(5,7)]<- paste0("counts_",c(x[1],x[2]));x1[2,5]<-8;x2<-data.frame(apply(cbind(x1[,5],x1[,7]),1,function(y) {chisq.test(y)$p.value})); colnames(x2)<- paste0("Counts_",x[1],x[2]);x2}) ####In the above code:, I replaced a count datapoint to make it significant for the purpose of separating the significant from others ( x1[2,5]<- 8). lst3<-lapply(lst2,function(x) {x1<-list(x[!x[,1]<0.05,],x[x[,1]<0.05,]);names(x1)<-rep(colnames(x),each=2);x1}) lst3[[5]] #$Counts_a2c3 #[1] 1 1 1 1 1 #$Counts_a2c3 #[1] 0.01963066 A.K. ________________________________ From: Vera Costa <veracosta...@gmail.com> To: arun <smartpink...@yahoo.com> Sent: Tuesday, March 26, 2013 4:26 PM Subject: Re: new question (if you could help...) But you could do the code of t test and chisq.test or not? Thank you No dia 26 de Mar de 2013 20:16, "arun" <smartpink...@yahoo.com> escreveu: ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.