Not sure I understand the problem. 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 0.21 0.1 0 0 0 XLOC_000006 0 0.1 0 0.01 0 0 XLOC_000007 0 0 0 0 1 3 XLOC_000008 0 0 0 0 0.15 0 XLOC_000009 0 0 0.12 0 0 0 XLOC_000010 7 1 5 3 0 1 XLOC_000011 63 10 19 15 92 228 ",sep="",stringsAsFactors=FALSE,header=TRUE) mat1<- as.matrix(dat1[,-1]) row.names(mat1)<- dat1[,1]
mat1[rowSums(mat1<=0.2)!=ncol(mat1),] ZPT.1 ZPT.0 ZPT.2 ZPT.3 PDGT.1 PDGT.0 XLOC_000001 3516 626.00 1277.0 770 4309 9030 XLOC_000002 342 82.00 185.0 72 835 1095 XLOC_000003 2000 361.00 867.0 438 454 687 XLOC_000004 143 30.00 67.0 37 90 236 XLOC_000005 0 0.21 0.1 0 0 0 ##row is selected because at least one of the element is >0.2 XLOC_000007 0 0.00 0.0 0 1 3 XLOC_000010 7 1.00 5.0 3 0 1 XLOC_000011 63 10.00 19.0 15 92 228 as.vector(which(!rowSums(mat1<=0.2)!=ncol(mat1))) #[1] 6 8 9 mat1[c(6,8,9),] # ZPT.1 ZPT.0 ZPT.2 ZPT.3 PDGT.1 PDGT.0 #XLOC_000006 0 0.1 0.00 0.01 0.00 0 #XLOC_000008 0 0.0 0.00 0.00 0.15 0 #XLOC_000009 0 0.0 0.12 0.00 0.00 0 A.K. ________________________________ From: Vivek Das <vd4mm...@gmail.com> To: arun <smartpink...@yahoo.com> Sent: Monday, August 5, 2013 1:05 PM Subject: Re: Removing the rows where all the elements are 0 Hi Arun, This seems to work only if the values are perfect 0 but if there are values in rows like 0.01, 0.08 and 0.05 then if I want to use the command res2<-mat1[rowSums(mat1<=0.2)!=ncol(mat1),] Then it does not work. Can you tell me why? Lets say I want to remove the rows which have values less than 0.2 for the columns then what should be the condition? ---------------------------------------------------------- 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 On Mon, Aug 5, 2013 at 2:31 PM, arun <smartpink...@yahoo.com> wrote: 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.
