MADSEq for mouse genome

[hagen-wende]

I'm trying to use MADSEQ for mouse aneuploidy, but I already get an error preparing coverage:

aneuploidy_cov = prepareCoverageGC(target_bed=target, bam=aneuploidy_bam, "mm39")
The error is:
Error in h(simpleError(msg, call)) : error in evaluating the argument 'subject' in selecting a method for function 'findOverlaps': object 'gap_gr' not found

Could it be that this is not working for mouse since there are only human gap_gr files in the installations (see attachment)?

Best
Hagen

[tabbzi]

To workaround missing GRanges objects expected by prepareCoverageGC() for non-human genomes, I had initialized empty GRanges objects in my R environment:

gap_gr <- GRanges()
HLA_gr <- GRanges()
AQP7_gr <- GRanges()

Perhaps not a proper solution but it did enable prepareCoverageGC() to run on my data. Better would be to get specific genomic regions for your genome's gaps, HLA locus, and... uh, aquaporin 7 (?)