[Bioc-sig-seq] Views on RleList, RangesList doesn't match elements up by name

[Aaron Statham]

Hi all,

Just a gotcha I ran into today - when running Views() on
RleList,RangesList arguments, the ranges are applied to the RleList by
order of the list, not by matching up names.
Consequently I had views running off the edge of a RleList with no
warning or error being thrown.

Example:
> rle1 <- RleList(chr1=Rle(1:50), chr2=Rle(1:10))
> ranges1 <- RangesList(chr2=IRanges(c(1,3), width=5), chr1=IRanges(c(5,15), width=5))
> rle1
SimpleRleList of length 2
$chr1
'integer' Rle of length 50 with 50 runs
  Lengths:  1  1  1  1  1  1  1  1  1  1  1 ...  1  1  1  1  1  1  1  1  1  1
  Values :  1  2  3  4  5  6  7  8  9 10 11 ... 41 42 43 44 45 46 47 48 49 50

$chr2
'integer' Rle of length 10 with 10 runs
  Lengths:  1  1  1  1  1  1  1  1  1  1
  Values :  1  2  3  4  5  6  7  8  9 10

> ranges1
SimpleRangesList of length 2
$chr2
IRanges of length 2
    start end width
[1]     1   5     5
[2]     3   7     5

$chr1
IRanges of length 2
    start end width
[1]     5   9     5
[2]    15  19     5

> Views(rle1, ranges1)
SimpleRleViewsList of length 2
$chr1
Views on a 50-length Rle subject

views:
    start end width
[1]     1   5     5 [1 2 3 4 5]
[2]     3   7     5 [3 4 5 6 7]

$chr2
Views on a 10-length Rle subject

views:
    start end width
[1]     5   9     5 [5 6 7 8 9]
[2]    15  19     5 [ ]

> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-07-06 r52460)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] IRanges_1.7.32

A quick fix would be to in RleViewsList() to check for names in
rleList & rangesList (as is done in findOverlaps methods) and reorder
one before the call to Map(Views, ...)

Cheers,
Aaron

--
Aaron Statham
Postgraduate Scholar, Cancer Epigenetics
Garvan Institute of Medical Research   Tel: (02) 9295 8393
384 Victoria St Darlinghurst 2010   Fax: (02) 9295 8316
NSW Australia         email: a.statham at garvan.org.au