[BioC] GRangesList replacement method bug

[Hervé Pagès]

Hi Richard,

On 11-12-14 02:01 PM, Richard Bourgon wrote:
> BioC team:
>
> I encountered a bug with replacement methods for GRangesList objects (see below for code).
>
> Basically, you can set to non-existant elementMetaData columns for a GRanges object, but not if it is a part of a GRangesList. Setting to already existing columns is fine, however.
>
> Richard Bourgon, Ph.D.
> Genentech, Inc.
> Bioinformatics&  Computational Biology
> 1 DNA Way, MS 93
> South San Francisco, CA 94080-4990
> (650) 467-2064
>
> ***
>
> gr<- GRanges( "a", IRanges(1,10), x = TRUE )
> grl<- GRangesList( y = gr, z = gr )
> values( grl[["y"]] )$x<- FALSE # Fine for existing column
> values( grl[["y"]] )$w<- FALSE # Fails for new column
>
> Error in .Method(..., deparse.level = deparse.level) :
> number of columns for arg 2 do not match those of first arg
>
> values( gr )$w<- FALSE # No problem with new column here

The error message doesn't help but this error is actually intended. This
is because all the individual GRanges elements in a GRangesList object
must have exactly the same columns (in the same order). For example,
you get the same error if you use the GRangesList() constructor to try
to put together 2 GRanges objects that don't have the same cols:

   > GRangesList(GRanges("a", IRanges(1,10), x=TRUE),
                 GRanges("a", IRanges(1,10)))
   Error in .Method(..., deparse.level = deparse.level) :
     number of columns for arg 2 do not match those of first arg

or if they have the same columns but not in the same order:

   > GRangesList(GRanges("a", IRanges(1,10), x=TRUE, w=2),
                 GRanges("a", IRanges(1,10), w=3, x=FALSE))
   Error in .Method(..., deparse.level = deparse.level) :
     column names for arg 2 do not match those of first arg

When you do 'values(grl[[1]])$w <- FALSE', you are trying to add a
column to the 1st GRanges in the GRangesList, but then its columns
would not be the same as those of the other elements anymore.
Note that if 'grl' has only 1 element, it works:

   > grl <- GRangesList(GRanges("a", IRanges(1,10)))
   > values(grl[[1]])$w <- FALSE
   > grl
   GRangesList of length 1:
   [[1]]
   GRanges with 1 range and 1 elementMetadata value:
         seqnames    ranges strand |         w
            <Rle> <IRanges>  <Rle> | <logical>
     [1]        a   [1, 10]      * |     FALSE

   ---
   seqlengths:
     a
    NA

Also note that you can always add, remove, shuffle, rename the columns
of all the elements in a GRangesList object by unlisting/relisting the
object. For example to add a "w" column to all the GRanges in 'grl':

   unlisted <- unlist(grl, use.names=FALSE)
   values(unlisted)$w <- FALSE
   relist(unlisted, grl)

More generally speaking, and maybe the name of the container doesn't
help, but conceptually a GRangesList object is not just a list of
arbitrary/unrelated GRanges objects. All the GRanges objects in the
GRangesList share the same columns and sequence levels.

Hope this help,
H.


> sessionInfo()
>
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8
> [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] datasets  utils     grDevices graphics  stats     methods   base
>
> other attached packages:
> [1] rtracklayer_1.14.4    RCurl_1.8-0           bitops_1.0-4.1        GenomicRanges_1.6.4
> [5] IRanges_1.12.5        gdata_2.8.2           BiocInstaller_1.2.1
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.14.0    Biostrings_2.22.0 BSgenome_1.22.0   gtools_2.6.2      tools_2.14.0
> [6] XML_3.6-2         zlibbioc_1.0.0
>
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

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