Thanks for this great package. I just have a question about the output of dba.count.
I'm trying to generate a count matrix with dba.count, but noticed a strange mixup with the coordinates. Attached below is a toy example that I hope clearly shows the issue.
consensus_peakset is a GRanges object of a peak set I retrieved using dba.peakset. I ran dba.count on a few peaks from 2 chromosomes (chr1, chr15). The resulting db$binding matrix has the same start and end coordinates, but the CHR column shows chromosomes 1 and 2. One of these must be incorrect.
I noticed the chromosome name format changed from 'chrX' to just 'X', and I imagine that has something to do with the reordering of factor levels. Am I doing something wrong, or is this a bug?
Thanks again for your help!