[BioC] IRanges::Rle and missing values
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Fri Aug 20 17:53:09 CEST 2010
Would it make sense to allow missing values in Rle objects and also to
incorporate removal of missing values in running summaries (and
possibly other functions)?
Example:
> tmp = Rle(c(1,2,2,2,3,NA,NA,NA,NA,2,3,3,3,3,3,2))
> tmp
'numeric' Rle of length 16 with 10 runs
Lengths: 1 3 1 1 1 1 1 1 5 1
Values : 1 2 3 NA NA NA NA 2 3 2
Seems like the run of 4 NA's is treated differently
> runsum(tmp, k = 2)
'numeric' Rle of length 15 with 11 runs
Lengths: 1 2 1 1 1 1 1 1 1 4 1
Values : 3 4 5 NA NA NA NA NA NA NA NA
And there is no way to do runsum(..., na.rm = TRUE) like in sum (as
far as I can see).
Kasper
> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-08-20 r52790)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
[3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
[5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915
[7] LC_PAPER=en_US.iso885915 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices datasets utils methods
[8] base
other attached packages:
[1] multicore_0.1-3 IRanges_1.7.19 matrixStats_0.2.1 R.methodsS3_1.2.0
[5] ggplot2_0.8.8 proto_0.3-8 reshape_0.8.3 plyr_1.1
loaded via a namespace (and not attached):
[1] tools_2.12.0
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