[Bioc-devel] coverage,GenomicRanges interpretation of 'weight'
hpages at fhcrc.org
Thu Feb 23 22:41:11 CET 2012
On 02/23/2012 11:13 AM, Cook, Malcolm wrote:
> It would be great I think if coverage,GenomicRanges interpetation of 'weight' would be similar to that for RangedData
> For 'RangedData' objects, this can also be a single string naming a column to be used as the weights.
> In the case for coverage,GenomicRanges we would want to weigh by any attribute (i.e. score) in the values DataTable.
> is this reasonable?
> I like being able to refer symbolically as provided by RangedData. It allows me to write, for instance, this utility function:
> ## PURPOSE: compute the coverage of x, split by 'strand'.
> ## RETURNS: a list of SimpleRLEList (by chromosome)
> which I can then use as
> Otherwise I would have to test for the presence of a weight attribute and split it by strand, and use mapply instead, etc....
> Regardless of the merits, having the interface to coverage be similar between RangedData and GenomicRanges is arguably desirable.
Sounds good to me. Done in GenomicRanges 1.7.27.
> My workaround is to convert to RangedData for the computation. Definitely not urgent.
> Malcolm Cook
> Bioc-devel at r-project.org mailing list
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