Hi David, Thanks for your reply! But what if I cannot change the positions of each row pairs in A. Sorry I did not make it very clear. The two columns in A represent start-and-end or end-and-start positions of a gene. The one column in B is the single nucleotide position . I am trying to index out all the single nucleotides that fall between the start and end region of a gene. Jiang > From: dcarl...@tamu.edu > To: dcarl...@tamu.edu; zhyjiang2...@hotmail.com; r-help@r-project.org > CC: sarah.gos...@gmail.com > Subject: RE: [R] Index out SNP position > Date: Thu, 3 Jan 2013 16:35:30 -0600 > > I missed the fact that the columns are not consistently smaller/larger: > > > A <- t(apply(A, 1, function(x) c(min(x), max(x)))) > > A > [,1] [,2] > [1,] 35838396 36151202 > [2,] 35838584 35838674 > [3,] 35838674 36003908 > [4,] 36003908 36004090 > [5,] 36003992 36150188 > > indx <- sapply(1:nrow(B), function(i) any(B[i]>A[,1] & B[i]<A[,2])) > > SNP <- B[indx] > > SNP > [1] 36003918 35838399 35838589 > > ------- > David > > > > -----Original Message----- > > From: David L Carlson [mailto:dcarl...@tamu.edu] > > Sent: Thursday, January 03, 2013 4:23 PM > > To: 'JiangZhengyu'; 'r-help@r-project.org' > > Subject: RE: [R] Index out SNP position > > > > Something like this? > > > > > indx <- sapply(1:nrow(B), function(i) any(B[i]>A[,1] & B[i]<A[,2])) > > > SNP <- B[indx] > > > SNP > > [1] 36003918 35838399 35838589 > > > > ---------------------------------------------- > > David L Carlson > > Associate Professor of Anthropology > > Texas A&M University > > College Station, TX 77843-4352 > > > > > -----Original Message----- > > > From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- > > > project.org] On Behalf Of JiangZhengyu > > > Sent: Thursday, January 03, 2013 3:55 PM > > > To: r-help@r-project.org > > > Subject: [R] Index out SNP position > > > > > > > > > > > > > > > > > > > > > > > > Dear R experts, > > > > > > I have 2 matix: A& B. I am trying to index B against A - (1) find out > > B > > > rows that fall between the col 1 and 2 of A& put them into a new > > > vector SNP.I made code as below, but I cannot think of a right way to > > > do it. Could anyone help me with the code? Thanks,Jiang---- > > > > > > A <- > > > > > matrix(c(35838396,35838674,36003908,36004090,36150188,36151202,35838584 > > > ,35838674,36003908,36003992), ncol = 2) > > > B <- matrix(c(36003918,35838399,35838589,36262559),ncol = 1) > > nr=nrow(A) > > > rn=nrow(B) for (i in 1:nr) > > > { > > > for (j in 1:rn){if (B[i,1]<=A[j,1] && B[i,1]>=A[j,2]){SNP[i]=B[i,1]}} > > > } > > > > > > [[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. > [[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.
