[Bioc-sig-seq] Fwd: seqselect using GRanges object on multiple chromosomes

[Janet Young]

Hi again,

A further note - the workaround I first emailed only works when there's one range per chromosome.   I have a better workaround now - the coercion looks like this instead:

convertGRangesToCompressedIRangesList <- function (myGRobject) {
    myGR_convert <- split(myGRobject, seqnames(myGRobject) )
    names(myGR_convert) <- unlist(lapply(myGR_convert, function(x) { as.character(seqnames(x))[1] }))
    
    myGR_convert <- lapply(myGR_convert, ranges )
    class(myGR_convert) <- "CompressedIRangesList"
    myGR_convert
}

Janet



Begin forwarded message:

> From: Janet Young <jayoung at fhcrc.org>
> Date: June 22, 2011 4:01:03 PM PDT
> To: Bioc-sig-sequencing at r-project.org
> Subject: seqselect using GRanges object on multiple chromosomes 
> 
> Hi there,
> 
> I'm updating some of my older code - I was previously storing regions of interest as RangedData but now I'm switching to GRanges.  I'm running into a little trouble with seqselect - I've found a workaround but wanted to suggest extending seqselect so it can work with GRanges objects directly.
> 
> I have some scores for each base-pair I've stored as a SimpleRleList object.  I want to use GRanges object with seqselect to pull out scores from my regions of interest, but to make that work I first have to do an odd (and slightly wrong-looking, to me) coercion of my GRanges object to a CompressedIRangesList.
> 
> I think the code below explains all (?).
> 
> thanks very much,
> 
> Janet
> 
> 
> 
> 
> 
>> library(GenomicRanges)
> Loading required package: IRanges
> 
> Attaching package: 'IRanges'
> 
> The following object(s) are masked from 'package:base':
> 
>    cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin,
>    pmin.int, rbind, rep.int, setdiff, table, union
> 
>> 
>> ### make some scores objects, for single chromosomes, or across several chrs
>> tempscores <- Rle(1:20)
>> tempscores2 <- Rle(101:120)
>> allscores <- RleList(chr1=tempscores,chr2=tempscores2) # yields a SimpleRleList
>> 
>> ## make some ranges objects
>> myIR <- IRanges(start=3,end=5)
>> myGR <- GRanges(seqnames=c("chr1","chr2"),ranges=IRanges(start=3,end=5))
>> myRD <- RangedData(space=c("chr1","chr2"),IRanges(start=c(3,3),end=c(5,5)) )
>> 
>> 
>> ### test seqselect:
>> seqselect(tempscores,myIR) #works
> 'integer' Rle of length 3 with 3 runs
>  Lengths: 1 1 1
>  Values : 3 4 5
>> seqselect(allscores,myGR) # doesn't work
> Error in seqselect(allscores, myGR) : unrecognized 'start' type
>> seqselect(allscores,myRD) # doesn't work
> Error in seqselect(allscores, myRD) : unrecognized 'start' type
>> 
>> seqselect(allscores,ranges(myRD)) # works. ranges(myRD) is a CompressedIRangesList
> SimpleRleList of length 2
> $chr1
> 'integer' Rle of length 3 with 3 runs
>  Lengths: 1 1 1
>  Values : 3 4 5
> 
> $chr2
> 'integer' Rle of length 3 with 3 runs
>  Lengths:   1   1   1
>  Values : 103 104 105
> 
>> 
>> seqselect(allscores,ranges(myGR)) # doesn't work
> Error in .bracket.Index(start, length(x), names(x), asRanges = TRUE) : 
>  range index out of bounds
>> seqselect(allscores,split(myGR)) # doesn't work
> Error in seqselect(allscores, split(myGR)) : unrecognized 'start' type
>> 
>> #### coerce myGR to something that looks a bit like a CompressedIRangesList
>> myGR_convert <- split(myGR)
>> names(myGR_convert) <- names(seqlengths(myGR_convert))
>> myGR_convert <- lapply(myGR_convert, ranges )
>> class(myGR_convert) <- "CompressedIRangesList"
>> 
>> 
>> seqselect(allscores,myGR_convert) # works
> SimpleRleList of length 2
> $chr1
> 'integer' Rle of length 3 with 3 runs
>  Lengths: 1 1 1
>  Values : 3 4 5
> 
> $chr2
> 'integer' Rle of length 3 with 3 runs
>  Lengths:   1   1   1
>  Values : 103 104 105
> 
>> 
>> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> 
> 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] GenomicRanges_1.4.6 IRanges_1.10.4     
> 
>