[BioC] subset a RleList using GRanges object?

[Janet Young]

Hi there,

I'm playing around with coverage data generated outside of R, planning to plot RNA-seq coverage for some genes we're interested in.

I have a request - it'd be nice from my point of view if it were possible to look at a small region an RleList (or CompressedRleList) using a GRanges object to focus on that smaller region.  Looks like I can subset a single Rle object with an IRanges object, but I wonder if this nice feature could be extended to GRanges objects?

Some code is below to show what I'm trying to do.

thanks veruy much,

Janet



library(GenomicRanges)

## an example RleList
x <- Rle(10:1, 1:10)
y <- Rle(10:1, 1:10)
z <- RleList( chr1=x, chr2=y)

## an example GRanges object
myRange <- GRanges( seqnames="chr1", ranges=IRanges(start=10,end=15) )

## subsetting an Rle using an IRanges object works, as expected:
z[["chr1"]] [ ranges(myRange) ] 

## but subsetting an RleList by GRanges object doesn't work
z [ myRange ] 
# Error in normalizeSingleBracketSubscript(i, x) : invalid subscript type

sessionInfo()

R Under development (unstable) (2013-11-06 r64163)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] GenomicRanges_1.15.10 XVector_0.3.2         IRanges_1.21.13      
[4] BiocGenerics_0.9.1   

loaded via a namespace (and not attached):
[1] stats4_3.1.0




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Dr. Janet Young 

Malik lab
http://research.fhcrc.org/malik/en.html

Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., A2-025, 
P.O. Box 19024, Seattle, WA 98109-1024, USA.

tel: (206) 667 4512
email: jayoung  ...at...  fhcrc.org

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