Problem with Mapped implementation of GenometriCorr

[Sam Arsenault]

Hello,

I am trying to compute the significance of the overlap between two sets of intervals that are both biased towards genic regions. Consequently, based on my reading of your documentation, I have tried to perform GenometriCorr on a mapped query and reference set. When I perform the MapRangesToGenomicIntervals function on the query and reference, I receive a large number of warnings such as:

"The chromosome scaffold223.2 is not normalised in where.to.map; skipped". 

Consequently, when I get to the GenometriCorrelation step, I receive the error:

"Error in GenometriCorrelation(mapped_DMRG, mapped_DEX, ecdf.area.permut.number = pn.area,  : 

  The query and reference have to have some common chromosome names, and they do not.

  It's all lost!"

I am working in a non-model system so the genome assembly is still scaffolded which I thought might account for the lack of normalisation but I was wondering if there was anything you could suggest to help me get around this problem?

I have included a directory with my files and script, if you would like to take a look at what I am doing. 

Thanks in advance,

Sam

[favorov]

It is fixed in 1.1.18

Thank you!