I got my gene annotation as a GRanges-object from Biomart. Now I try to count the reads from a bamfile using this annotation with the bamCount function from the bamsignals package. Unfortunately this otherwise excellent function gives me an
Error: chromosome chrY not present in the bam file
(no surprise, since the data comes from a woman). Since I look at more bamfiles which are from men and women, I'd like something like NA for the chrY gene counts. What would be the best way to tackle this problem? I'm sure I'm not the first one to encounter a woman.