Question: ranges input for GenomicFiles
1
22 months ago by
Qiang70
Qiang70 wrote:

Hi,

I am working on a function with VCF/variants and BAM as input. The reduceByFile/reduceByRange are imported in my function, which require GRanges/GRangesList as ranges input.

However, my input requires a extented GRanges class with variants(DNAStringSet) in elementMetadata, like, CollapsedVCF.

Is it possible to extented the ranges arguments? for example, classes inherited from GRanges?

Thanks!

genomicfiles • 335 views
modified 22 months ago by Martin Morgan ♦♦ 24k • written 22 months ago by Qiang70
1
22 months ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:

If you're asking about package development, then the bioc-devel mailing list is the correct place. Generally, method dispatch should work to the  'nearest' class, so if the class you are interested in contains (in S4 language) a class that is in the signature of the method you want to use, then things should 'just work'. If they do not  work, then more detail is required, in particular a reproducible example. For a package, this might require going so far as to create a small package as a github repository that captures the problem.

1

Thank you for your reply. Because my input require extra data for each range. I guess I could extend a GRanges class with extra elementMetadata as input for my function, but convert it back to GRanges when using reduceBy functions.