[BioC] IRanges::Rle and missing values

[Kasper Daniel Hansen]

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