[Bioc-sig-seq] Update only specific spaces of RangedData

[Patrick Aboyoun]

Michael,
Now that the constituent parts of RangedData (RangesList and 
SplitDataFrameList) have '[<-' methods, it should be straight-forward to 
add a '[<-' operator for RangedData. However, since the ranges are 
modified by

ranges(x)[i] <- value

I find the

values(x)[i,j] <- value

approach to be a nice complement.


Patrick


Michael Lawrence wrote:
>
>
> On Fri, Sep 25, 2009 at 1:40 AM, Patrick Aboyoun <paboyoun at fhcrc.org 
> <mailto:paboyoun at fhcrc.org>> wrote:
>
>     Christian,
>     Thanks for bringing this issue up. I have been meaning to improve
>     the subscript replacement functions in IRanges for some time and
>     this gives me a reason to make some improvements now. I need to
>     put some testing infrastructure in place to ensure the software is
>     behaving as expected, but the current solution I am working on for
>     your problem would look like
>
>     values(x)[[i]][[j]] <- value    # set the jth column in the ith space
>
>     As this operation shows, I am working on the values table of the
>     RangedData object and not the whole object. This will complement
>     the current method of selecting the jth column in the ith space
>
>     values(x)[[i]][[j]]    # get the jth column in the ith space
>
>     I'll let you know when this enhancement has been check-in.
>
>
> Is there any reason why
>
> > x[i][[j]] <- value
>
> Would not work? I mean, RangedData just needs to support '[<-'.
>
> Michael
>  
>
>
>     Patrick
>
>
>
>
>     Christian Ruckert wrote:
>
>         I am missing a method to update only specific spaces of a
>         RangedData object.
>
>         Let 'x' be a 'RangedData' object.
>
>         The two existing methods are:
>
>         'x[i]': Subsets 'x' by indexing into its spaces, so the result is
>                  of the same class, with a different set of spaces.
>
>         'x[[j]] <- value': Sets value as column 'j' in 'x', where 'j' can
>                  be a character, numeric, or logical scalar that
>         indexes into
>                  the columns. The length of 'value' should equal
>         'nrow(x)'.
>
>         I am looking for a mixture of both, something like:
>
>         x[i][[j]] <- value
>
>         which actually doesn't work this way.
>
>         Any help would be appreciated,
>         Christian
>
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