While I tend to agree with you that PCA is too big an operation to be hidden
within a plotting function (MDS is an edge-case I would say), I can’t see how
we can ever reach a point where there is only one generic plot function. In the
case of PCA there is a number of different plot-types that
Thank you Hervé! I failed to realized that this was included in the docs.
Anyhow, we've been discussing internally what default value to use. We
also noted that the `genomecov` tool from BED in it's split mode
ignores the D's:
http://bedtools.readthedocs.org/en/latest/content/tools/genomecov.html
Hello,
In my `derfinder` package I have been relying on `GenomeInfoDb` to
correctly name the sequence names. Given
https://support.bioconductor.org/p/62136/ I now realize that I was
expecting too much from `GenomeInfoDb`.
For example, in some cases I was expecting it to guess that a single
'2'
