Hi,
bg<- read.table(text=" Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125 Otu00131 Otu00137 Otu00155 Otu00158 Otu00172 Otu00181 Otu00185 Otu00190 Otu00209 Otu00218 Gi20Jun11 0.001217 0 0.001217 0 0.000000 0 0 0 0.001217 0 0 0 0 0 0.001217 0 0.001217 Gi40Jun11 0.000000 0 0.000000 0 0.000000 0 0 0 0.000000 0 0 0 0 0 0.000000 0 0.000000 Gi425Jun11 0.000000 0 0.000000 0 0.000000 0 0 0 0.000000 0 0 0 0 0 0.000000 0 0.000000 Gi45Jun11 0.000000 0 0.000000 0 0.001513 0 0 0 0.000000 0 0 0 0 0 0.000000 0 0.000000 Gi475Jun11 0.000000 0 0.000000 0 0.000000 0 0 0 0.000000 0 0 0 0 0 0.000000 0 0.000000 Gi50Jun11 0.000000 0 0.000000 0 0.000000 0 0 0 0.000000 0 0 0 0 0 0.000000 0 0.000000 ",sep="",header=TRUE,stringsAsFactors=F) c_bg<- read.table(text=" Otu00039 Otu0128 Otu0218 Otu0034 Otu00158 Otu0257 Otu0212 Otu00125 ",sep="",header=FALSE,stringsAsFactors=F) bg[,names(bg)%in%c_bg[,1]] # Otu00039 Otu00125 Otu00158 #Gi20Jun11 0.001217 0 0 #Gi40Jun11 0.000000 0 0 #Gi425Jun11 0.000000 0 0 #Gi45Jun11 0.000000 0 0 #Gi475Jun11 0.000000 0 0 #Gi50Jun11 0.000000 0 0 A.K. ----- Original Message ----- From: Ozgul Inceoglu <ozgul.inceo...@ulb.ac.be> To: r-help@r-project.org Cc: Sent: Tuesday, February 12, 2013 9:29 AM Subject: [R] subsetting data file by intoducing a second file Hello, I have a very data matrix and I have a file which has the names that I need to subset. However I cannot manage to subset the main file. ANy idea? bg <- read.table (file.choose(), header=T, row.names) bg Otu00022 Otu00029 Otu00039 Otu00042 Otu00101 Otu00105 Otu00125 Otu00131 Otu00137 Otu00155 Otu00158 Otu00172 Otu00181 Otu00185 Otu00190 Otu00209 Otu00218 Gi20Jun11 0.001217 0 0.001217 0 0.000000 0 0 0 0.001217 0 0 0 0 0 0.001217 0 0.001217 Gi40Jun11 0.000000 0 0.000000 0 0.000000 0 0 0 0.000000 0 0 0 0 0 0.000000 0 0.000000 Gi425Jun11 0.000000 0 0.000000 0 0.000000 0 0 0 0.000000 0 0 0 0 0 0.000000 0 0.000000 Gi45Jun11 0.000000 0 0.000000 0 0.001513 0 0 0 0.000000 0 0 0 0 0 0.000000 0 0.000000 Gi475Jun11 0.000000 0 0.000000 0 0.000000 0 0 0 0.000000 0 0 0 0 0 0.000000 0 0.000000 Gi50Jun11 0.000000 0 0.000000 0 0.000000 0 0 0 0.000000 0 0 0 0 0 0.000000 0 0.000000 ... #second file which has the names that I want to subset c_bg [,1] [1,] "Otu0128" [2,] "Otu0218" [3,] "Otu0034" [4,] "Otu0257" [5,] "Otu0212" [6,] "Otu0279" [7,] "Otu0318" [8,] "Otu0266" [9,] "Otu0056" ... #by using the c_bg name file, I would like to subset bg file g1<-subset(bg,colnames(bg) %in% (c_bg)) # this returns me the all the column names in bg file. Thank you, Ö ______________________________________________ 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.