remove NA's from a DelayedArray
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maltethodberg ▴ 140
@maltethodberg-9690
Last seen 4 weeks ago
Denmark

Given that subsetting works slightly different for a DelayedArray compared to a matrix, is there a good alternative to m[is.na(m)] <- 0 for replacing NA's in  a DelayedArray?

delayedarray • 598 views
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@herve-pages-1542
Last seen 5 hours ago
Seattle, WA, United States

Hi,

I need to think of a more natural/intuitive way to support this but in the mean time you can use the following:

replaceNAs <- function(x, value)
{
    stopifnot(is(x, "DelayedArray"),
              is.vector(value),
              is.atomic(value),
              length(value) == 1L)
    DelayedArray:::register_delayed_op(x,
        function(xx) ifelse(is.na(xx), value, xx)
    )
}

Then:

library(DelayedArray)
A <- DelayedArray(matrix(c(NA, 1:10, NA), ncol=3))

A
# DelayedMatrix object of 4 x 3 integers:
#      [,1] [,2] [,3]
# [1,]   NA    4    8
# [2,]    1    5    9
# [3,]    2    6   10
# [4,]    3    7   NA

replaceNAs(A, 0)
# DelayedMatrix object of 4 x 3 logicals:
#      [,1] [,2] [,3]
# [1,]    0    4    8
# [2,]    1    5    9
# [3,]    2    6   10
# [4,]    3    7    0

Cheers,

H.

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After more thoughts on this, I think we can support delayed subassignment (i.e. x[i] <- value) at least in the special case where: (1) i is a logical DelayedArray with the same dimensions as x, and (2) value is a scalar (i.e. atomic vector of length 1). That would cover x[is.na(x)] <- 0 but also things like x[x == 0.6] <- NA or x[x > 0 & log(x) < 0.5] <- -1 etc...

I'll try to get this in the DelayedArray package today or tomorrow.

H.

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I added this to DelayedArray 0.3.20:

library(DelayedArray)
A <- DelayedArray(matrix(c(NA, 1:10, NA), ncol=3))
A[is.na(A)] <- 0
A
# DelayedMatrix object of 4 x 3 doubles:
#      [,1] [,2] [,3]
# [1,]    0    4    8
# [2,]    1    5    9
# [3,]    2    6   10
# [4,]    3    7    0

DelayedArray 0.3.20 should become available in BioC devel via biocLite() in the next 24 hours or so.

Cheers,

H.

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cool thanks!

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