Make macs3 groupby parameter optional

[GirayEryilmaz]

Greetings,

I am relatively new to atac-seq analysis and I was wondering, why is the groupby parameter obligatory in the macs3 peak calling function? I took a subset of cells from the whole dataset and I would like to call peaks on that subset. So I don't have groups to group-by. Am I missing something?

Thank you!

[kaizhang]

With 'groupby', you don't have to manually subset the dataset. You can call peaks for each cell type/group in one run and is much more efficient. If you want to call peaks on whole dataset, you just need to add a pseudo group by, for example, data.obs['group'] = '1'. If this turns out to be a very common case, I may consider support this directly in macs3.

[kaizhang]

Implemented in 4abc7b7