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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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Find DARs between different samples #141

Open esh81 opened 4 years ago

esh81 commented 4 years ago

Hi,

Is there any way to find DARs between different samples (ie, compare DARs between different samples as opposed to different clusters)? I've read in my different samples into one snap file and called peaks for each sample, but can't figure out how to get the DARs because there is a cluster.pos option but not a sample option in the findDAR step.

Thank you!

billzt commented 4 years ago

I also have the same needs. However after reviewing the code of https://github.com/r3fang/SnapATAC/blob/master/R/findDARs.R, it is just simple usage of DGEList from package edgeR, therefore I'll try to modify it to suit for samples