I just checked in some changes to IRanges, that make this method work:
setMethod("resize", "GenomicRanges",
function(x, width, fix = "start", use.names = TRUE)
{
revFix <- c(start = "end", end = "start", center = "center")
fix <- ifelse(strand(x) == "-", revFix[fix], fix)
ranges <-
resize(ranges(x), width = width, fix = fix, use.names =
use.names)
if (!IRanges:::anyMissing(seqlengths(x))) {
start(x) <- start(ranges)
end(x) <- end(ranges)
} else {
x <- clone(x, ranges = ranges)
}
x
}
)
That will accept the fix argument, except start and end are reversed for
negative strand features. '*' is treated just like '+'. If this is
acceptable to the GenomicRanges guys, I will commit this.
On Tue, Sep 14, 2010 at 9:36 AM, Ivan Gregoretti <[email protected]> wrote:
> 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
> <[email protected]> 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
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-sig-sequencing mailing list
> > [email protected]
> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >
>
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