[Bioc-devel] GenomicFiles: some random issues

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Mon Sep 29 04:49:28 CEST 2014

(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]
 RleList of length 1
 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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