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 < [email protected]> 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. > > [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
