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

[Tim Yates]

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?

Thanks!

Tim Yates 
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