[Bioc-sig-seq] seqselect on SimpleRleList and RangesList - bug? and request

[Janet Young]

Hi,

I've been playing around with seqselect on scores stored in a  
SimpleRleList object to get subregions defined in a RangesList object.

I found a couple of things:  first an enhancement request - would it  
be possible to allow seqselect to deal with cases where not every  
space (name) in the SimpleRleList has a corresponding space/name in  
the RangesList object?

The second is either bug or else I've misunderstood the way seqselect  
is supposed to work, in a dangerous way - it looks like seqselect  
doesn't use the names of the list items to select scores, it just  
assumes that in the two lists the elements have the same names in the  
same order.

The code below should explain both issues problem much better than  
those descriptions.

thanks,

Janet



 > library(IRanges)

Attaching package: 'IRanges'

The following object(s) are masked from 'package:base':

     cbind, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,  
rbind, rep.int, table

 >
 > ### generate some arbitrary scores
 > track <- RangedData(RangesList(chrA = IRanges(start = c(1, 4, 6),  
width=c(3, 2, 4)),chrB = IRanges(start = c(1, 3, 6), width=c(3, 3,  
4))) )
 > trackCoverage <- coverage(track,  
weight=list(chrA=c(2,7,3),chrB=c(1,1,1)) )
 >
 > ### define subregions
 > exons <- RangesList(chrA = IRanges(start = c(2, 4), width =  
c(2,2)),chrB = IRanges(start = 3, width = 5))
 >
 > ### seqselect works if all spaces in trackCoverage have an element  
in exons
 > seqselect(trackCoverage,exons )
SimpleRleList of length 2
$chrA
'integer' Rle of length 4 with 2 runs
   Lengths: 2 2
   Values : 2 7

$chrB
'integer' Rle of length 5 with 2 runs
   Lengths: 1 4
   Values : 2 1

 >
 > ### define subregions only on one chr
 > exons_chrAonly <- RangesList(chrA = IRanges(start = c(2, 4), width  
= c(2, 2)))
 > ### now seqselect doesn't work if some spaces don't have any elements
 > seqselect(trackCoverage,exons_chrAonly )
Error in seqselect(trackCoverage, exons_chrAonly) :
   'length(start)' must equal 'length(x)' when 'end' and 'width' are  
NULL
 >
 >
 > ##### also, defining the regions with spaces in a different order  
seems to cause trouble as seqselect doesn't seem to be using the  
list's names - just going by order of elements
 > exons_reorderchrs <- RangesList(chrB = IRanges(start = 3, width =  
5),chrA = IRanges(start = c(2, 4), width = c(2,2)))
 > seqselect(trackCoverage,exons_reorderchrs )
SimpleRleList of length 2
$chrA
'integer' Rle of length 5 with 3 runs
   Lengths: 1 2 2
   Values : 2 7 3

$chrB
'integer' Rle of length 4 with 3 runs
   Lengths: 1 1 2
   Values : 1 2 1

 >
 > identical ( seqselect(trackCoverage,exons ) ,  
seqselect(trackCoverage,exons_reorderchrs )  )
[1] FALSE
 >
 > sessionInfo()
R version 2.11.1 (2010-05-31)
i386-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] IRanges_1.6.6