Hi,

I'm currently using Diffbind for my ATAC-seq pipeline. After calling the dba.analyze function you can do various plots via e.g. dba.plotMA. But is there some simple way to extract the logFoldChange, pvalues etc from the DBA object? I guess this should be easy since the object obviously stores the values for plotting, but I just cant seem to find where.

Cheers,

JB

Hi,

dba.report is the function you want.  It has about 20 parameters controlling exactly what you get, but with default parameters (and the dba object) it'll give you p-value, FDR, logFC, etc for the first contrast.  Have a read through the manual for dba.report to see other options.

Cheers,

 - Gord