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vplagnol / ExomeDepth

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
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Vignette and documentation for bin.length of select.reference.set are inconsistent #28

Open bpow opened 4 years ago

bpow commented 4 years ago

The documentation for select.reference set defines bin.length as "Length (in bp) of each of the regions" (my emphasis).

However, the vignette gives as an example for bin.length:

bin.length = (ExomeCount.dafr$end - ExomeCount.dafr$start)/1000

... which looks to me to be the length in kb rather than bp. Which should it be, or does it not matter as long as it is proportional for all of the regions?

Also-- since ExomeCount.dafr is derived from a GRanges object, I think these are 1-based inclusive coordinates, so the bin.length would be more accurately ExomeCount.dafr$end - ExomeCount.dafr$start + 1) (adding 1), right?

bpow commented 4 years ago

I'd be happy to submit a pull request to correct either the vignette or the documentation for select.reference, but don't know which one might need to be edited.