unclear how "covers" is defined

[ShanEllis]

In matchGenes(), in both the description and region values of the output, there is a "covers" category. I'm trying to pinpoint in the code exactly what this means, but I'm having trouble tracking it down. Is this for genomic regions that cannot be defined in any of the other categories? Or something else?

[sampoll]

Hi ShanEllis,

If you execute:

df <- matchGenes(bumps, features)

and get an output row that says your bump "covers" a feature, it means that your bump is a superset of the feature, i.e., its start position on the strand is less than the features start position and its end position is larger than the feature's end position.

The "region" column then says "covers" too, because the region is the same; it's not upstream or downstream or "overlaps 3' end" or anything like that.

Is that your question?

• Sam