[Bioc-devel] Meta data access with $ for GRanges vs RangedData vs data.frame

[Hervé Pagès]

Hi Tim and other $ fans,

On 03/19/2012 05:02 AM, Tim Yates wrote:
> Hi all,
>
> I have a feeling I asked this before, but cannot find the mail, or the answer I received, so sorry if we're covering old ground.
>
> I have a package which can deal with data.frames, RangedData objects or Granges objects.
>
> Assuming I have:
>
> library( IRanges )
> library( GenomicRanges )
>
> # Setup a data.frame
> df = data.frame( start=c( 1, 2 ),
>                   end=c( 3, 4 ),
>                   strand=c( '+', '+' ),
>                   name=c( 'tim', 'yates' ),
>                   more=c( T, F ) )
> # Setup a RangedData object
> rd = as( df, 'RangedData' )
> # Setup a GRanges object
> gr = as( rd, 'GRanges' )
>
> Then the following is the behaviour when trying to use $ for accessing the column 'name':
>
> print( df$name )
> # [1] tim   yates
> # Levels: tim yates
>
> print( rd$name )
> # [1] tim   yates
> # Levels: tim yates
>
> print( gr$name )
> # Error in gr$meta : $ operator not defined for this S4 class
>
> Using it for assignment also gives problems:
>
> df$foo = c( 'bar', 'baz' )
> # Adds new column 'foo' to df with values 'bar' and 'baz'
> rd$foo = c( 'bar', 'baz' )
> # Adds new column 'foo' to rd with values 'bar' and 'baz'
> gr$foo = c( 'bar', 'baz' )
> # Error in `$<-`(`*tmp*`, "foo", value = c("bar", "baz")) :
> #  no method for assigning subsets of this S4 class
>
> Now, if I add the following two methods to my code:
>
> `$.GRanges`   = function( x, name )        {
>    elementMetadata( x )[[ name ]]
> }
> `$<-.GRanges` = function( x, name, value ) {
>    elementMetadata( x )[[ name ]] = value
>    x
> }
>
> Then all the above functions behave in a similar fashion, however I don't want to do this in my package, as I believe it will be a gateway to namespace hell…
>
> Is there any plan to add this accessor operator to Granges so that access is normalised across all three of these types?

Yes. Actually our plan for BioC 2.11 is to use € for this, not $,
for obvious reasons.

Cheers,
H.

>
> Thanks!
>
> Tim Yates
> --------------------------------------------------------
> This email is confidential and intended solely for the...{{dropped:22}}