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eonurk / cinaR

A differential and enrichment analyses pipeline for bulk ATAC-seq (and RNA-seq)
https://eonurk.github.io/cinaR/
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Differential Analyses - final.matrix #7

Closed cmf1997 closed 1 year ago

cmf1997 commented 1 year ago

hello there, cinaR is a wonderful tools for analysis ATAC-seq I was wondering what is format of final.matrix (Annotated Consensus peaks) I was trying to conducting Differential Analyses in my custom peak matrix with custom annotation and I want to conduct Differential Analyses only rather than cinaR much appreciated if you can provide any information

eonurk commented 1 year ago

You could find more information about this in Get Started vignette.

Cheers, Onur

cmf1997 commented 1 year ago

thanks for your quick response in the get started page, there is a original bed file that is unannotated but it seems that Annotated Consensus peaks file format that required for da is not present

eonurk commented 1 year ago

Yes, if you give cinaR the non-annotated matrix, it will create it for you in the final object

cmf1997 commented 1 year ago

exactly but i now want to conduct differential analysis only as reference mentioned `da i have a consensus peak set annotated by custom txdb so it doesn't match mm10 or hg19 …

the input of differential analysis is Annotated Consensus peaks i was confusing the format

cmf1997 commented 1 year ago

is the Annotated Consensus peaks format was bed-like, such counts of different groups in consensus peak set with additional column that contain annotated information

eonurk commented 1 year ago

CinaR doesn't have support for other txdbs yet, but it would be awesome if you would like to contribute to the project!

cmf1997 commented 1 year ago

i checked the original code of cinaR.R and solved the problem thanks again! it now support custom txdb i would make it more elegant and commit~