Vincent Plagnol
Vincent Plagnol
> Hey , I got this result @ CNV.calls :'data.frame': 0 obs. of 0 variables > > so what happened ? I think it makes sense if there is no...
Long standing issue, but looking into this now as I refresh the package. Do you know if Bioconductor has written tools to parse CRAM files? I see no mention in...
Thanks all- FWIW I'd be happy to add CRAM support if the underlying Rsamtools library was upgraded, it's clearly a very nice to /must have. Anything else would be painful...
I am thinking as I am writing here, so apologies for any silliness. Packaging the samtools binary seems painful because it's an external binary, and creates all sort of issues...
Yes from the vignette I wrote ages ago I see `getBAMCounts creates an object of the GRanges class which can easily be converted into a matrix or a data frame...
Thanks I am looking into this now. That issue is now keeping ExomeDepth out of CRAN so I need to work it out.
OK I think it's sorted. The explanation came from this post: https://stat.ethz.ch/pipermail/r-package-devel/2022q4/008580.html ExomeDepth should be back in CRAN shortly (or so I hope).
And @Leelouh if you can give the latest version of the repo a try, it would be a good confirmation that the issue is fixed.
Can you try now? It works for me nicely but I have been doing some work on the package so it is plausible that you picked up the package at...
Thanks. First of all the package is now back on CRAN, so I can think of adding other bits. Do you want to send me a pull request with the...