CODEWITHSUNDEEP
rloopsmatrixsum
user1357015
user1357015

Reputation: 11696

creating a sum matrix from counts

I have one matrix of mutation counts, say "counts". This matrix has column names V1, V2,...,Vi,...Vn where not every "i" is there. Thus it can jump, such as V1, V2, V5 say. Further, most of columns have a 0 in them.

I need to create a sum matrix, called "answer", where element i, j is the sum of the number of the number counts at both i and j. At the i, i element it just shows the number of counts at i.

Here's a quick data set up. I already have the correct dimensioned matrix set up in my code called "answer". Thus what I would need to automate are the last several lines where I fill in the matrix.

counts <- matrix(data = c(0,2,0,5,0,6,0), nrow = 1, ncol = 7,    dimnames=list("",c("V1","V2","V3","V4","V5","V6","V7")))

answer <- matrix(data =0, nrow = 3, ncol = 3, dimnames = list(c("V2","V4","V6"),c("V2","V4","V6")))

answer[1,1] <- 2
answer[1,2] <- 7
answer[1,3] <- 8
answer[2,1] <- 7
answer[2,2] <- 5
answer[2,3] <- 11
answer[3,1] <- 8
answer[3,2] <- 11
answer[3,3] <- 6

I understand I can do this with 2 nested for loops, but surely there must be a better way no? Thanks!

Upvotes: 4

Views: 271

Answers (1)

David Robinson
David Robinson

Reputation: 78620

This could be done with the right use of expand.grid and rowSums:

n = counts[, counts > 0]
answer = matrix(rowSums(expand.grid(n, n)), nrow=length(n), dimnames=list(names(n), names(n)))
diag(answer) = n

To show how it works, n would end up being:

V2 V4 V5 
 2  5  6

and expand.grid(n, n) would be:

  Var1 Var2
1    2    2
2    5    2
3    6    2
4    2    5
5    5    5
6    6    5
7    2    6
8    5    6
9    6    6

The last line (diag) is necessary because otherwise the diagonal would be twice the original vector (adding 2+2, 5+5, or 6+6).

Upvotes: 4

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