extracting gene coordinates from AnnotationByGeneParts object

[ghost]

Hi,

I have been exploring your package for annotation, and have a question:

When we use annotateWithGeneParts, it outpus a AnnotationByGeneParts object which primarily contains promoter/exon/intron/intergenic percentages. However, is there a way to take it a step further, and extract which CpG sites (or whatever data is being used as the target) with the annotation results along with at least the gene name?

Thus, for each site, can we extract the original data from target plus the region which it falls upon and gene name? It seems to me that this data should already be stored somewhere given the calculation of how much fall within each feature, but I cannot find it.

The closest I got to what I would ideally want is to use getAssociationWithTSS, but as the functions suggests this only gets us the closest TSS and not what region "promoter/exon/intron/intergenic"

Thank you so much!

[al2na]

you can use simple GenomicRanges functions for that. Have a look at here http://compgenomr.github.io/book/genomicIntervals.html

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On Tue, Jun 4, 2019 at 11:28 PM lshepard2154 ***@***.***> wrote: Hi, I have been exploring your package for annotation, and have a question: When we use annotateWithGeneParts, it outpus a AnnotationByGeneParts object which primarily contains promoter/exon/intron/intergenic percentages. However, is there a way to take it a step further, and extract which CpG sites (or whatever data is being used as the target) with the annotation results along with at least the gene name? Thus, for each site, can we extract the original data from target plus the region which it falls upon and gene name? It seems to me that this data should already be stored somewhere given the calculation of how much fall within each feature, but I cannot find it. The closest I got to what I would ideally want is to use getAssociationWithTSS, but as the functions suggests this only gets us the closest TSS and not what region "promoter/exon/intron/intergenic" Thank you so much! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#186?email_source=notifications&email_token=AAE32EP2GCAGSQEZTDOQWSTPY3NAJA5CNFSM4HTD6XJ2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4GXUI2NQ>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAE32ENKVKLOKULQVLJWWPDPY3NAJANCNFSM4HTD6XJQ> .

[ghost]

Hello Altuna,

Thank you for letting me know about this resource (and the time you took to write it). Very useful! I will be digging into the other chapters as well, looks great.