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GreenleafLab / 10x-scATAC-2019

Publication Page for Satpathy*, Granja* et al 2019
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unable to find an inherited method for function ‘NSBS’ for signature ‘"standardGeneric"’ #1

Closed pangxueyu233 closed 5 years ago

pangxueyu233 commented 5 years ago

Hello, It's really an awsome wroking. But I got a error by using your workflow in 01_Filter_Cells_v2, as following:

fragments <- fragments[mcols(fragments)[,by] %in% rownames(tssSingles)[tssSingles$cellCall==1]] Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘NSBS’ for signature ‘"standardGeneric"’

I don't know the ### mcols(fragments)[,by] meaning, and I got error in this formula. Hope you could help me out.

Thanks

pangxueyu233 commented 5 years ago

And I tried to change the code like this:

fragments <- fragments[mcols(fragments)[,"RG"] %in% rownames(tssSingles)[tssSingles$cellCall==1]]

And it works, I know this step wants to filter cells but I'm not sure whether it's right by my fixing.

pangxueyu233 commented 5 years ago

One more suggestion, could you upgrade the codes? Because some parts was used Seurat V2.3, it's not friendly to further people using seurat V3. Thanks

jeffmgranja commented 5 years ago

looks like a variable got deleted

by = "RG"

i normally write it as mcols(fragments)$RG but i corrected it everywhere to be more flexible