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]]
Assuming I understand what you want, which I'm not certain of, here's one way; there are more (probably some more elegant). I'm not sure how you'd put them in a vector, since there are different numbers of values for each row of A, so instead I've made a list. unlist(SNP) will turn it into a vector. It's also not consistent which column of A has the higher and lower values. SNP <- lapply(seq_len(nrow(A)), function(x)B[B >= min(A[x,]) & B <= max(A[x,])])> SNP[[1]] [1] 36003918 35838399 35838589 [[2]] [1] 35838589 [[3]] numeric(0) [[4]] [1] 36003918 [[5]] numeric(0) On Thu, Jan 3, 2013 at 4:54 PM, JiangZhengyu <zhyjiang2006 at hotmail.com> wrote:> > > > > > > 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]}} > } >-- Sarah Goslee http://www.functionaldiversity.org
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-bounces at r-project.org [mailto:r-help-bounces at r- > project.org] On Behalf Of JiangZhengyu > Sent: Thursday, January 03, 2013 3:55 PM > To: r-help at 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 at 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.
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:dcarlson at tamu.edu] > Sent: Thursday, January 03, 2013 4:23 PM > To: 'JiangZhengyu'; 'r-help at 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-bounces at r-project.org [mailto:r-help-bounces at r- > > project.org] On Behalf Of JiangZhengyu > > Sent: Thursday, January 03, 2013 3:55 PM > > To: r-help at 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 at 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.
On Jan 3, 2013, at 1:54 PM, JiangZhengyu wrote:> > > > > > > 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]}} > }> sapply(B, function(x) apply(A, 1, function(two) x %in% two[1]:two[2]))[,1] [,2] [,3] [,4] [1,] TRUE TRUE TRUE FALSE [2,] FALSE FALSE TRUE FALSE [3,] FALSE FALSE FALSE FALSE [4,] TRUE FALSE FALSE FALSE [5,] FALSE FALSE FALSE FALSE So the first and third B-locations are in the range of two of the rows, the second-B in one range and the third is in none of them. There is also a bioconductor package called `IRanges` that will undoubtedly be more efficient. (This works because the problem is of necessity dealing with integers.) -- David Winsemius Alameda, CA, USA