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Peak GC content quantification in ATAC module #54

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emdann opened this issue Apr 8, 2022 · 1 comment
Open

Peak GC content quantification in ATAC module #54

emdann opened this issue Apr 8, 2022 · 1 comment
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atac Related to the muon.atac module enhancement New feature or request

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@emdann
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emdann commented Apr 8, 2022

Hi there,

First of all, every time I go back to working with muon it gets better and better, so thanks for the great work!

I was wondering whether you had thought of adding a muon.atac.pp function to compute GC content of peaks. This is frequently used for peak-gene association testing (e.g. here), and as far as I am aware there is no easy functionality in python for this (I've always used addGCBias from chromVAR in R).

@emdann emdann added the enhancement New feature or request label Apr 8, 2022
@gtca
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gtca commented Apr 26, 2022

Thank you, @emdann!

Thanks for raising this, we plan to improve how peak sequences are operated indeed. That should include GC content.
Currently, there's ac.tl.get_sequences to get a list of strings (a sequence for each peak) and one can start with calculating G and C fractions from that. (We will probably refactor things here but a similar function will still be available.)

@gtca gtca added the atac Related to the muon.atac module label Jul 1, 2022
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Labels
atac Related to the muon.atac module enhancement New feature or request
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