[Bioc-sig-seq] Resizing a GRanges object with elements on the "*" strand

[Ivan Gregoretti]

Hello Leonardo,

I believe that the issue here is that resize() does not support the
"fix" argument at all when handling GRanges.

Actually that would be a nice upgrade of functionality for GRanges.

I face the same limitation and I currently resize by hand. :(

This is my work around:

library(GenomicRanges)

# a set of genomic features called C
C <- GRanges(seqnames=c("chr1","chr2","chr19","chrX"),
             ranges=IRanges(start=c(0,0,5,1),
                            end=c(150,150,150,400)),
             strand=c("*","-","*","+"),
             score=c(10,20,30,90))


# peek at C
C
GRanges with 4 ranges and 1 elementMetadata value
    seqnames    ranges strand |     score
       <Rle> <IRanges>  <Rle> | <numeric>
[1]     chr1  [0, 150]      * |        10
[2]     chr2  [0, 150]      - |        20
[3]    chr19  [5, 150]      * |        30
[4]     chrX  [1, 400]      + |        90

seqlengths
  chr1 chr19  chr2  chrX
    NA    NA    NA    NA

# this is the workaround
ranges(C) <- resize(ranges(C),1,fix="start")

# peek at the resized set C
C
GRanges with 4 ranges and 1 elementMetadata value
    seqnames    ranges strand |     score
       <Rle> <IRanges>  <Rle> | <numeric>
[1]     chr1    [0, 0]      * |        10
[2]     chr2    [0, 0]      - |        20
[3]    chr19    [5, 5]      * |        30
[4]     chrX    [1, 1]      + |        90

seqlengths
  chr1 chr19  chr2  chrX
    NA    NA    NA    NA


Cheers,

Ivan


Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1016 and 1-301-496-1592
Fax: 1-301-496-9878



On Tue, Sep 14, 2010 at 11:36 AM, Leonardo Collado Torres
<lcollado at ibt.unam.mx> wrote:
> Hello,
>
> I have a rather simple question that involves GenomicRanges' design.
>
> Basically, I have a GRanges object where all the elements are from the
> undefined "*" strand. I just want to resize them to get the 1st (from left
> to right) base. However, I'm not able to do so with the "resize" function
> even when specifying fix = "start" as it uses the fix = "center" method. Is
> this the desired performance? I have 2 workarounds, but I'm puzzled as the
> "flank" function actually uses the start (left to right) when elements are
> from the "*" strand. Is there a quicker way to do this or should I stick to
> the flank + shift workaround?
>
> Thank you and greetings,
> Leonardo
>
>> testGR <- GRanges( seqnames = rep("test", 3), ranges = IRanges ( start =
> c(10,100,1000), width = c(10, 100, 1000)), strand = Rle(strand(c("+","-")),
> c(1,2)) )
>> testGR
> GRanges with 3 ranges and 0 elementMetadata values
>    seqnames       ranges strand |
>       <Rle>    <IRanges>  <Rle> |
> [1]     test [  10,   19]      + |
> [2]     test [ 100,  199]      - |
> [3]     test [1000, 1999]      - |
>
> seqlengths
>  test
>   NA
>> resize(testGR, 1, fix="start")
> GRanges with 3 ranges and 0 elementMetadata values
>    seqnames       ranges strand |
>       <Rle>    <IRanges>  <Rle> |
> [1]     test [  10,   10]      + |
> [2]     test [ 199,  199]      - |
> [3]     test [1999, 1999]      - |
>
> seqlengths
>  test
>   NA
>> testGR2 <- GRanges( seqnames = rep("test", 3), ranges = IRanges ( start =
> c(10,100,1000), width = c(10, 100, 1000)), strand = Rle(strand(c("*")),
> c(3)) )
>> testGR2
> GRanges with 3 ranges and 0 elementMetadata values
>    seqnames       ranges strand |
>       <Rle>    <IRanges>  <Rle> |
> [1]     test [  10,   19]      * |
> [2]     test [ 100,  199]      * |
> [3]     test [1000, 1999]      * |
>
> seqlengths
>  test
>   NA
>> resize(testGR2, 1, fix="start")
> GRanges with 3 ranges and 0 elementMetadata values
>    seqnames       ranges strand |
>       <Rle>    <IRanges>  <Rle> |
> [1]     test [  14,   14]      * |
> [2]     test [ 149,  149]      * |
> [3]     test [1499, 1499]      * |
>
> seqlengths
>  test
>   NA
>
>> testGR3 <- GRanges ( seqnames = seqnames(testGR2), ranges = IRanges( start
> = start(testGR2), width = 1), strand = strand(testGR2) )
>>
>> testGR3
> GRanges with 3 ranges and 0 elementMetadata values
>    seqnames       ranges strand |
>       <Rle>    <IRanges>  <Rle> |
> [1]     test [  10,   10]      * |
> [2]     test [ 100,  100]      * |
> [3]     test [1000, 1000]      * |
>
> seqlengths
>  test
>   NA
>>
>
>> testGR4 <- shift(flank( testGR2, 1), 1)
>> testGR4
> GRanges with 3 ranges and 0 elementMetadata values
>    seqnames       ranges strand |
>       <Rle>    <IRanges>  <Rle> |
> [1]     test [  10,   10]      * |
> [2]     test [ 100,  100]      * |
> [3]     test [1000, 1000]      * |
>
> seqlengths
>  test
>   NA
>
>> sessionInfo()
> R version 2.12.0 Under development (unstable) (2010-09-08 r52880)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>  [7] LC_PAPER=en_US.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GenomicRanges_1.1.25 IRanges_1.7.33
>
> loaded via a namespace (and not attached):
> [1] tools_2.12.0
>
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>
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