[Bioc-devel] coverage,GenomicRanges interpretation of 'weight'

[Cook, Malcolm]

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:

coverageByStrand <-function(x,...){
  ## PURPOSE: compute the coverage of x, split by 'strand'. 
  ## RETURNS: a list of SimpleRLEList (by chromosome)
  res<-lapply(split(x,strand(x)),coverage,...)
}

which I can then use as

someStrandedCoverage<-coverageByStrand(someStrandedFeaturesAsGenomicRanges,weight='theDataTableAttributeHoldingSomeWeightFactor')

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.

My workaround is to convert to RangedData for the computation.  Definitely not urgent.

Malcolm Cook