Why do other chromosomes appear when you only import chr1 as your selection of interest from bigwig file?

[yeungj234]

In this problem, I am only selecting to import a specific region from chromosome 1, but why do other chromosomes still appear in the RleList even though they have a value of 0 since they weren't imported?

[matthew-paul-2006]

I think in the import bigwig the information about the different chromosomes is derived from the headers in the bigwig, not our subsetted GRange. So that means even though we don't have other chromosome sequence imported, the list slots are still made for each chromosome with the length information.

A simple way around this is just to drop the chromosomes you don't care about by subsetting the RLElist down to the chromosomes you care about. In this case we could just do:

bigWigPeaks <- bigWigPeaks$chr1