Question

colMax is not exported from the xcms package

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Habil Zare ▴ 200

@habil-zare-7836

Last seen 13 months ago

United States/Austin Area

The colMax() function from the xcms package is very useful and even has good documentation, but why is it not exported?! Are there alternatives to "Find row and column maximum values for numeric arrays"?


library(xcms)
a1 <- array(1:(2*3*5),dim=c(5,3,2))
xcms:::colMax(a1)
     [,1] [,2]
[1,]    5   20
[2,]   10   25
[3,]   15   30
colMax(a1)
Error in colMax(a1) : could not find function "colMax"
?colMax


sessionInfo()
R Under development (unstable) (2021-01-28 r79891)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] xcms_3.13.8         MSnbase_2.17.7      ProtGenerics_1.23.9
[4] S4Vectors_0.29.9    mzR_2.25.5          Rcpp_1.0.6         
[7] Biobase_2.51.0      BiocGenerics_0.37.1 BiocParallel_1.25.5

xcms • 1.6k views

ADD COMMENT • link 3.6 years ago Habil Zare ▴ 200

score 0 · Answer 1 · 2021-05-20

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Entering edit mode

Mike Smith ★ 6.6k

@mike-smith

Last seen 2 days ago

EMBL Heidelberg

I haven't looked at the xcms implementation, but for your example could achieve this with apply() and max() performed over the 2nd and 3rd dimensions e.g.

> apply(a1, MARGIN = c(2,3), FUN = max)
     [,1] [,2]
[1,]    5   20
[2,]   10   25
[3,]   15   30

ADD COMMENT • link 3.6 years ago Mike Smith ★ 6.6k

0

Entering edit mode

xcms implemented it in c, which is 50 times faster than apply():

> a2 <- array(1:(10^7*3*5),dim=c(5,3,10^7))
> system.time(xcms:::colMax(a2))
   user  system elapsed 
  1.086   0.524   1.614 
> system.time(apply(a2, MARGIN = c(2,3), FUN = max))
   user  system elapsed 
 51.347   3.386  54.776

ADD REPLY • link 3.6 years ago Habil Zare ▴ 200