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 <ivangreg@gmail.com> 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
> <lcollado@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
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-sig-sequencing mailing list
> > Bioc-sig-sequencing@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >
>
> _______________________________________________
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>

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