Is it possible to create a new dba object based on a subset of the samples in a previous call to dba.count, or dba.analyze?
Basically, I would like analyze subsets of samples as seperate analyses, without recounting. I'm analyzing atac-seq data, which is paired end and >50 million reads per sample for 20-30 samples. I've been using the summarize overlaps method to count (bSummarizeOverlaps=TRUE), which works great but takes a lot of time even on a server.
A second and related question: is there a way to pull out a summarizedExperiment from dba.report without limiting to a specific contrast (or with all contrasts)? I'm trying to get all of my samples into a summarizedExp object, using the counts and peaks data in the dba object.
Thanks for the great package!