Nearest Genes Function

[nleroy917]

Given a query and set of annotations, this function will calculate
the nearest annotation to each region in the region set, as well
as the nearest gene type and the distance to the nearest gene.

This is updated from the previous version which wasn't functioning
properly!

The only issue I am having is that the function requires that the
annotation file has the name of the gene defined as gene_id
and the type of gene as gene_biotype. It would be nice to
introduce a keyword parameter that defaults to these two,
but can be changed to extract out this information should an
annotation file be given with different schema or naming convention.

However, I am having a hard time attempting to dynamically access these attributes. For example:

query$gene_type = annotation[nearestIds]$gene_type

versus

query$gene_type = annotations[nearestIds][key_name]

[kkupkova]

The function gives error. There is definitely a typo - check "annotation" and "annotations". Please test that the function works before you give it to check. Also, I don't think it would work with GRangesList at this point (check how all the other functions include code for GRangesList objects).

[nsheff]

Did you confirm that this works with GRangesList objects?

[nsheff]

I see now this was closed in favor of #172

It's good to put a note here for future reference.