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p4rkerw / Muto_Wilson_NComm_2020

Workflow for analysis of healthy human kidney by snRNAseq and snATACseq
MIT License
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annotate DARs for each cell type #3

Closed linhch5 closed 3 years ago

linhch5 commented 3 years ago

Hi, Dr. Wilson and Dr. Muto: Thank you very much for providing your code to working with the snATAC-seq analysis. The following error appeared when I was using your code to annotate the cell type specific DAR. Do you know why and how can I solve the problem?

list.peakAnno <- lapply(list.dar.gr, annotatePeak, TxDb = txdb,tssRegion = c(-3000, 3000), verbose = FALSE) Error in which(strand(subject) != "-") : argument to 'which' is not logical 1621005341(1)

p4rkerw commented 3 years ago

Hello,

Thanks for checking out our repo! It’s hard to know exactly what the problem is without a reproducible example but I have a few ideas for you to try out. I think the issue is that the strand variable in your granges object is set to “*” instead of “+” or “-“. That might throw an error like the one you’re describing. Try changing the strand variable for all the data to “+” and run the function again. You might also want to check out the chipseekr website for additional info.

Parker

p4rkerw commented 3 years ago

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