R: fast determine top k maximum value in a matrix

Question

I would like to fast determine top k maximum values in a matrix, and then put those not the top k maximum value as zero, currently I work out the following solution. Can somebody improve these one, since when the matrix have many many rows, this one is not so fast?

thanks.

mat <- matrix(c(5, 1, 6, 4, 9, 1, 8, 9, 10), nrow = 3, byrow = TRUE)
sortedMat <- t(apply(mat, 1, function(x) sort(x, decreasing = TRUE, method =    "quick")))
topK <- 2
sortedMat <- sortedMat[, 1:topK, drop = FALSE]
lmat <- mat
for (i in 1:nrow(mat)) {
  lmat[i, ] <- mat[i, ] %in% sortedMat[i, ]
}
kMat <- mat * lmat

 > mat
 [,1] [,2] [,3]
[1,]    5    1    6
[2,]    4    9    1
[3,]    8    9   10

> kMat
     [,1] [,2] [,3]
[1,]    5    0    6
[2,]    4    9    0
[3,]    0    9   10

I don't see what this would have to do with Rcpp so I removed the `rcpp` tag you had there. — Dirk Eddelbuettel, Mar 23 '15 at 23:18
@DirkEddelbuettel He probably wants a faster version with `rcpp` — DatamineR, Mar 23 '15 at 23:19
Does this help you? http://stackoverflow.com/questions/2453326/fastest-way-to-find-second-third-highest-lowest-value-in-vector-or-column — Alex, Mar 23 '15 at 23:20
@DirkEddelbuettel. I just want to know if have a smarter way to do this. Not asking for code. Thanks. — BioChemoinformatics, Mar 23 '15 at 23:56

score 3 · Answer 1 · answered Nov 04 '18 at 19:25

3

In Rfast the command sort_mat sorts the columns of a matrix, colOrder does order for each column, colRanks gives ranks for each column and the colnth gives the nth value for each column. I believe at least one of them suit you.

answered Nov 04 '18 at 19:25

Mike

106
5

1

The code: `mat * (rowRanks(mat) > 1)` is OK. Thanks @Mike. – BioChemoinformatics Nov 09 '18 at 19:09

score 1 · Accepted Answer · answered Mar 24 '15 at 07:38

You could use rank to speed this up. In case there are ties, you would have to decide on a method to break these (e.g. ties.method = "random").

kmat <- function(mat, k){
  mat[t(apply(mat, 1, rank)) <= (ncol(mat)-k)] <- 0
  mat
}
kmat(mat, 2)
##      [,1] [,2] [,3]
## [1,]    5    0    6
## [2,]    4    9    0
## [3,]    0    9   10

R: fast determine top k maximum value in a matrix

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