[Bioc-devel] a pattern to be avoided? mcols(x)$y <- z

[Vincent Carey]

The following comes up in use of Fdb.InfiniumMethylation.hg19::getPlatform


debug: mcols(GR)$channel <- Rle(as.factor(mcols(GR)$channel450))

Browse[3]> system.time(uu <- Rle(as.factor(mcols(GR)$channel450)))

   user  system elapsed

  0.020   0.003   0.022

Browse[3]> system.time(mcols(GR)$channel <-
Rle(as.factor(mcols(GR)$channel450)))

   user  system elapsed

 47.263   0.067  47.373

Browse[3]> GR$channel[1]

factor-Rle of length 1 with 1 run

  Lengths:    1

  Values : Both

Levels(3): Both Grn Red

Browse[3]> system.time(GR$channel <- Rle(as.factor(mcols(GR)$channel450)))

   user  system elapsed

  0.058   0.006   0.065


Presumably the mcols()$<- copies/rewrites a lot of data needlessly?

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