[BioC] Selecting elements in GRanges object by element metadata

[Kasper Daniel Hansen]

What you are reporting is true for any (well, there may be exceptions
I guess) subsetting.  Try for example with a standard matrix.  The
solution is to add which().  Contrast

> x = c(1,2,NA)
> x == 2
[1] FALSE  TRUE    NA
> which(x == 2)
[1] 2

Kasper

On Wed, Jul 11, 2012 at 11:09 AM, Michael Muratet
<mmuratet at hudsonalpha.org> wrote:
> Greetings
>
> I would like to select elements from a GRanges object by testing values in
> the metadata columns. This seems to work OK:
>
> x.gr[which(elementMetadata(x.gr)$fdr<0.05)]
>
> So does this, although there's nothing in the documentation about the []
> operator accepting logical values:
>
> fosl2.th17.gr[elementMetadata(fosl2.th17.gr)$fdr<0.05]
>
> The problem arises when I try to select from a GRanges object where the
> metadata columns have NAs:
>
>> tss.annot.gr[na.omit(elementMetadata(tss.annot.gr)$GENE>0),"GENE"]
> GRanges with 4028 ranges and 1 elementMetadata col:
>          seqnames                 ranges strand   |   GENE
>             <Rle>              <IRanges>  <Rle>   |    <numeric>
>      [1]     chr1   [ 3659579,  3662079]      -   |         <NA>
>      [2]     chr1   [ 4847394,  4849894]      +   |            0
>      [3]     chr1   [10025979, 10028479]      -   |         <NA>
>      [4]     chr1   [17085879, 17088379]      -   |         <NA>
>      [5]     chr1   [21067298, 21069798]      -   |         <NA>
>      [6]     chr1   [21949662, 21952162]      -   |            0
>      [7]     chr1   [23388014, 23390514]      -   |         <NA>
>      [8]     chr1   [23768264, 23770764]      +   |         <NA>
>      [9]     chr1   [23927128, 23929628]      -   |         <NA>
>      ...      ...                    ...    ... ...          ...
>   [4020]     chr2 [126607180, 126609680]      -   |            0
>   [4021]     chr2 [127345106, 127347606]      -   |            0
>   [4022]     chr2 [129195132, 129197632]      +   | -1.223140339
>   [4023]     chr2 [129194856, 129197356]      -   | -1.628782357
>   [4024]     chr2 [129360338, 129362838]      -   | -1.475535653
>   [4025]     chr2 [129837609, 129840109]      +   |            0
>   [4026]     chr2 [129948520, 129951020]      +   |            0
>   [4027]     chr2 [140213446, 140215946]      -   |            0
>   [4028]     chr2 [148267271, 148269771]      -   | -1.564551101
>
> The values returned violate the condition. It won't work at all without
> na.omit.
>
> I can coerce the GRanges object to a data.frame, do the selection and create
> a new GRanges object, but I'm hoping there is a way to do it directly.
>
> Am I using the syntax correctly? Is there something peculiar about a
> DataFrame vs a data.frame that's getting in the way?
>
> Thanks
>
> Mike
>
>
>
> Michael Muratet, Ph.D.
> Senior Scientist
> HudsonAlpha Institute for Biotechnology
> mmuratet at hudsonalpha.org
> (256) 327-0473 (p)
> (256) 327-0966 (f)
>
> Room 4005
> 601 Genome Way
> Huntsville, Alabama 35806
>
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