Hi Vivek, dat1<- read.table(text=" gene ZPT.1 ZPT.0 ZPT.2 ZPT.3 PDGT.1 PDGT.0 XLOC_000001 3516 626 1277 770 4309 9030 XLOC_000002 342 82 185 72 835 1095 XLOC_000003 2000 361 867 438 454 687 XLOC_000004 143 30 67 37 90 236 XLOC_000005 0 0 0 0 0 0 XLOC_000006 0 0 0 0 0 0 XLOC_000007 0 0 0 0 1 3 XLOC_000008 0 0 0 0 0 0 XLOC_000009 0 0 0 0 0 0 XLOC_000010 7 1 5 3 0 1 XLOC_000011 63 10 19 15 92 228 ",sep="",stringsAsFactors=FALSE,header=TRUE)
res<- dat1[rowSums(dat1[,-1]==0)!=(ncol(dat1)-1),] res # gene ZPT.1 ZPT.0 ZPT.2 ZPT.3 PDGT.1 PDGT.0 #1 XLOC_000001 3516 626 1277 770 4309 9030 #2 XLOC_000002 342 82 185 72 835 1095 #3 XLOC_000003 2000 361 867 438 454 687 #4 XLOC_000004 143 30 67 37 90 236 #7 XLOC_000007 0 0 0 0 1 3 #10 XLOC_000010 7 1 5 3 0 1 #11 XLOC_000011 63 10 19 15 92 228 If it is a matrix: mat1<- as.matrix(dat1[,-1]) row.names(mat1)<- dat1[,1] res2<-mat1[rowSums(mat1==0)!=ncol(mat1),] res2 # ZPT.1 ZPT.0 ZPT.2 ZPT.3 PDGT.1 PDGT.0 #XLOC_000001 3516 626 1277 770 4309 9030 #XLOC_000002 342 82 185 72 835 1095 #XLOC_000003 2000 361 867 438 454 687 #XLOC_000004 143 30 67 37 90 236 #XLOC_000007 0 0 0 0 1 3 #XLOC_000010 7 1 5 3 0 1 #XLOC_000011 63 10 19 15 92 228 #I don't have an account in stackoverflow. So, it is must be somebody else. A.K. ________________________________ From: Vivek Das <vd4mm...@gmail.com> To: arun <smartpink...@yahoo.com> Sent: Monday, August 5, 2013 6:31 AM Subject: Removing the rows where all the elements are 0 Hi Arun, Am using a matrix of gene expression, frag counts to calculate differentially expressed genes. I would like to know how to remove the rows which have values as 0. Then my data set will be compact and less spurious results will be given for the downstream analysis I do using this matrix. Input gene ZPT.1ZPT.0ZPT.2ZPT.3PDGT.1PDGT.0XLOC_000001 3516626127777043099030XLOC_000002 34282185728351095XLOC_000003 2000361867438454687XLOC_000004 14330673790236XLOC_000005 000000XLOC_000006 000000XLOC_000007 000013XLOC_000008 000000XLOC_000009 000000XLOC_000010 715301XLOC_000011 6310191592228 Desired output gene ZPT.1ZPT.0ZPT.2ZPT.3PDGT.1PDGT.0XLOC_000001 3516626127777043099030XLOC_000002 34282185728351095XLOC_000003 2000361867438454687XLOC_000004 14330673790236XLOC_000007 000013XLOC_000010 715301XLOC_000011 6310191592228 As of now I only want to remove those rows where all the frag count columns are 0 if in any row some values are 0 and others are non zero I would like to keep that row intact as you can see my example above. Please let me know how to do this. Hey arun I did not understand the command you wrote in the R stack overflow forum can you plase write here and help me out. ---------------------------------------------------------- Vivek Das PhD Student in Computational Biology Giuseppe Testa's Lab European School of Molecular Medicine IFOM-IEO Campus Via Adamello, 16 Milan, Italy emails: vivek....@ieo.eu vchris...@yahoo.co.in vd4mm...@gmail.com ______________________________________________ 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.
