On Mon, Sep 20, 2010 at 3:56 PM, Martin Morgan <[email protected]> wrote:
> On 09/14/2010 01:46 PM, Michael Lawrence wrote:
> > 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.
>
> Yes this is acceptable; I'm cc'ing Herve as we were talking about this
> just this morning. Martin
>
>
Great. I will commit it after I fix my GenomicRanges which I broke with some
other changes....
> >
> > 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
> >>>
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> >>>
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> >>>
> >>
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> >
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