[R] Index out SNP position

[David Winsemius]

On Jan 3, 2013, at 1:54 PM, JiangZhengyu wrote:

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> Dear R experts,
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> 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----
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> 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