Custom regions in assignChromosomeRegion?
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Roger • 0
@roger-12673
Last seen 1 day ago
Netherlands

To whom it may concern,

The vignettes of ChIPpeakAnno include an image that seems to suggest that it is possible to assign peaks to regions other than the default ones, namely microRNAs and tRNAs. However, there is no explanation anywhere in this respect, so I was wondering whether it is an actual feature or just a mistake in the picture.

Besides, I would like to remind the developers that "Enhancer.Silencer" remains present in the documentation as part of the information contained in the resulting vector (it should be Intergenic.Region).

Best regards,

Roger

chippeakanno • 435 views
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Ou, Jianhong ★ 1.2k
@ou-jianhong-4539
Last seen 9 weeks ago
United States

Hi Roger,

Thank you for reporting the bugs. I will fix the documentation soon.

About the microRNAs and tRNAs, it depends on the TxDb object. The program will try to extract the microRNA and tRNA by methods GenomicFeatures::microRNAs and GenomicFeatures::tRNAs from TxDb object. If there is no return from those methods, they will be dropped.

Jianhong.

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