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

Cook, Malcolm MEC at stowers.org
Thu Feb 23 20:22:37 CET 2012

Another way the interface to coverage could/should agree between GenomicRanges and RangedData is the expectation of how width is encoded.

For GenomicRanges   "'width' must be NULL or a numeric vector"
For RangedData, "  'width' must be a non-empty list"

Of course not crucial.  But, the disagreement is easy to trip over.


> -----Original Message-----
> From: bioc-devel-bounces at r-project.org [mailto:bioc-devel-bounces at r-
> project.org] On Behalf Of Cook, Malcolm
> Sent: Thursday, February 23, 2012 1:14 PM
> To: 'bioc-devel at r-project.org'
> Subject: [Bioc-devel] coverage,GenomicRanges interpretation of 'weight'
> 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='theDa
> taTableAttributeHoldingSomeWeightFactor')
> 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
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