toGRanges() no longer working in response to UCSC update about chippeakanno HOT 3 CLOSED

A quick update on the situation: based on the responses in the linked GitHub issue, I used the patched version of GenomeInfoDb and received a different set of errors+warnings.

Calling toGRanges() produces no errors, but the following warning: cannot switch some of GRCm38's seqlevels from NCBI to UCSC style. If this annotation data is used with annotatePeakInBatch(), this warning appears: not all the seqnames of myPeakList is in the AnnotationData.The 2 combined objects have no sequence levels in common.

Lastly, attempting to add gene ID's and feature names to these peaks with addGeneIDs() fails entirely, with the error Error: There is no feature column in annotatedPeak or annotatedPeak has size 0!

I hope this provides some useful context, thank you in advance for your help!

from chippeakanno.

Hi,

Thank you for reporting this. I patched the package to handle this error. Please try to update the package to development version and try it again. Let me know if you still have question.

Jianhong.

from chippeakanno.

Hi Jianhong,

Your patch worked great! Thank you so much for fixing it, you have saved a critical component of my analysis.

-Jared

from chippeakanno.