HI,
?list.files() list.files() #created 4 files in my working directory #[1] "A_hubs.txt" "A_nonhubs.txt" "B_hubs.txt" "B_nonhubs.txt" #If you want to do wilcox.test in a pairwise manner: combn(list.files(),2) # [,1] [,2] [,3] [,4] #[1,] "A_hubs.txt" "A_hubs.txt" "A_hubs.txt" "A_nonhubs.txt" #[2,] "A_nonhubs.txt" "B_hubs.txt" "B_nonhubs.txt" "B_hubs.txt" # [,5] [,6] #[1,] "A_nonhubs.txt" "B_hubs.txt" #[2,] "B_nonhubs.txt" "B_nonhubs.txt" P_value<- sapply(as.data.frame(combn(list.files(),2),stringsAsFactors=FALSE),function(x){ x1<-read.table(x[1],sep="",header=TRUE); x2<- read.table(x[2],sep="",header=TRUE); wilcox.test(x1$TIS_SV,x2$TIS_SV)$p.value}) NAME<-gsub("[.txt]","",apply(as.data.frame(combn(list.files(),2),stringsAsFactors=FALSE),2, paste,collapse="_")) res<- data.frame(NAME,P_value,stringsAsFactors=FALSE) row.names(res)<-1:nrow(res) res # NAME P_value #1 A_hubs_A_nonhubs 0.3684845 #2 A_hubs_B_hubs 0.1388408 #3 A_hubs_B_nonhubs 0.1531984 #4 A_nonhubs_B_hubs 0.7910863 #5 A_nonhubs_B_nonhubs 0.4926012 #6 B_hubs_B_nonhubs 0.6350055 A.K. ----- Original Message ----- From: anupam sinha <anupam.cont...@gmail.com> To: r-help@r-project.org Cc: Sent: Tuesday, September 3, 2013 6:58 AM Subject: [R] reading files Dear all, I need help with some coding. I have a directory with files like these: A_hubs A_nonhubs B_hubs B_nonhubs : : Each of these files have the following header and content: GENE TIS_DEG TOT_SV TIS_SV TIS_DISO ensg1 20 12 4 40 . . and so on... I want to calculate the p-value of the function wilcox.test(A_hubs$TIS_SV,A_nonhubs$TIS_SV) and store it in a table of the format NAME p-value A 0.05 Can some give me pointers in the direction? Thanks in advance Anupam [[alternative HTML version deleted]] ______________________________________________ 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. ______________________________________________ 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.