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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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How to excess data plotted with CoveragePlot #32

Closed berixD closed 4 years ago

berixD commented 4 years ago

Hi timoast, Signac is a great tool. Thanks for that! I would like to extract the normalized accessibility data for all identities as plotted with CoveragePlot. With this data, I would like to know all regions of open chromatin (above a certain threshold) in order to look for cis-acting elements. I tried looking at the functions buildup and came up with the idea to use the cutmat matrix. But I am stuck, because I dont know how to do it for all identities and multiple regions in an efficient way.

Thanks in advance!

Ps. Is a command list of the signac package avialable? Something similar to Seurat's one would be nice https://satijalab.org/seurat/essential_commands.html

timoast commented 4 years ago

Hi, I think the easiest thing for you to do might be to call peaks on each group of cells and then quantify reads in those peaks using the FeatureMatrix function. You can write the cell names for each group to a file and then split the bam file by into different file for each group of cells using sinto, and then call peaks using the split bam files.

I don't have a command list for the package available right now, but I will add this to my list of things to do for Signac.

berixD commented 4 years ago

Thanks for the quick reply! I will try the FeatureMatrix option:)