Hi,It is not very clear. data1 <- read.table("PGRTvsPDGRT_frags.txt",header=TRUE,stringsAsFactors=FALSE) mat1<- as.matrix(data1[,-1]) row.names(mat1)<- data1[,1] res <- mat1[apply(mat1,1,function(x) all(x[1:6]!=0) & all(x[7:12]!=0)),] sum(rowSums(!res)>0) #[1] 0
#or #depending upon what you want res1 <- mat1[apply(mat1,1,function(x) all(x[1:6]!=0) | all(x[7:12]!=0)),] dim(res1) #[1] 12750 12 A.K. On Thursday, January 2, 2014 7:47 AM, Vivek Das <vd4mm...@gmail.com> wrote: Dear Users, I have few queries. I am having a matrix with some counts. there are 2 conditions for each. So I have a matrix with 12 columns with counts. First column is the id and next 6 columns are one condition and the second 6 columns are another condition. I want to remove the rows where each condition is having one 0 column. So for a rows if in both the conditions have one single 0 (which means each condition is having a 0 value) then that row is removed. How can we do that. I was doing like this earlier but we are left with some rows. data1<- read.table("~/Desktop/Bonn_New_Pas_algo_data/results_30092013/edgeR_24122013/PGRTvsPDGRT/PGRTvsPDGRT_frags.txt",header=TRUE,stringsAsFactors=FALSE) mat1<- as.matrix(data1[,-1]) row.names(mat1)<- data1[,1] test <- apply(mat1, 1,function(x) all(x[1:6]==0) | all(x[7:12]==0) ) test1 <- mat1[!test,] But this does not seem correct as I am having some rows like XLOC_004048 26.0133 0 0 0 0 232.296 2.676 8.21482 2.61507 0 0 0 XLOC_004050 0 1 4 36 20 0 0 2 1 0 1 9 This should not be there. Even if both condition together is having one column as zero in each condition in a row then it should be removed. but here we can see more than one column is having 0 values in both condition and still it is there. The the matrix I am working upon is in attachment. Can anyone give any suggestions ---------------------------------------------------------- Vivek Das ______________________________________________ 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.