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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