[Bioc-devel] GenomicFiles: some random issues

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Mon Sep 29 05:01:05 CEST 2014

7. It is surprising to me that BigWigFileViews does not inherit from
GenomicFiles, so I cannot call reduceByXX on it.  On the other hand,
coverage() works on it.

On Sun, Sep 28, 2014 at 10:49 PM, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:

> (not sure if stuff like this goes here or on the support site)
> I have started to experiment with the package.  Here are a couple of
> initial reactions.
> 1. Why does the return object of reduceByFile vs reduceByRange (with
> summarize = FALSE) different?  I understand why internally you have
> different nesting schemes (files and ranges) for the two functions, but it
> is not clear to me that it is desirable to have the return object depend on
> how the computation was done.
> 2. I think BigWigFileViews etc. should be mentioned in the vignette.
> There should be an example of GenomicFiles which is printed.
> 3. (well, this is GenomicRanges) It seems like GenomicFiles has a lot of
> similarities with SummarizedExperiment.  I have a lot of use cases for a
> simple class which has a single GRanges slot, and then support stuff like
> granges(), start(), end() etc.  Right now I have an implementation in
> bsseq:hasGRanges, but I think it could be widely useful and fits naturally
> with SummarizedExperiment.
> 4. coverage(BigWigFileViews) returns a "wrong" assay object in my opinion,
> it looks like
> > assay(tmp)[1,1]
>  $`unionpks:1`
>  RleList of length 1
>  $chr1
>  numeric-Rle of length 739 with 84 runs
>    Lengths:                 1                 3 ...                12
>    Values :  1.29999995231628  1.20000004768372 ...  1.39999997615814
> Specifically, each (i,j) entry in the object is an RleList with a single
> element with a name equal to the seqnames of the i'th entry in the query
> GRanges.  To me, this extra nestedness is unnecessary; I would have
> expected an Rle instead of an RleList with 1 element.
> 5. The return object of reduceByRange / reduceByFile with summarize = TRUE
> is a SummarizedExperiment with an unnamed assay.  I was surprised to see
> that this is even possible.
> 6. In the vignette, section 5.1, page 7, it seems weird to me that a Views
> is instantiated on the rle.

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