How to specify the parameters when using distal peaks for gene activity matrix

stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data

https://stuartlab.org/signac/

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How to specify the parameters when using distal peaks for gene activity matrix #186

Closed sylestiel closed 4 years ago

sylestiel commented 4 years ago

Hi,

Is it okay to provide a range for upstream and leave the downstream as 0 if we would like to use distal peaks as a measure of gene activity in the integration of scATAC with scRNA seq datasets?

Thanks!

timoast commented 4 years ago

Sure, the Extend function just extends the given ranges by the amount you want. You can change the upstream and downstream values to whatever suits your purpose.