3 months ago by
CRUK, Cambridge, UK
There is a sites parameter to some of the plotting functions to limit plots to a specific subset (using a logical vector), but no direct way to limiting an analysis using a logical vector of sites.
In the specific case you mention, where sites are limited to regions that overlap in a subset of samples, there are several ways to accomplish that. For example, you can generate a new DBA object with a subset of peaks by calling
dba() with a mask of peaksets and specify a
minOverlap (how many of those peaksets a regions should be called in). If you wanted to use these overlapping (or consensus) peaks for an analysis involving other peaksets, you can save the consensus peakset using
bRetrieve=TRUE and supply that as the value for the
peaks parameter in the call to
dba.count(). Likewise, you can retrieve the global peakset and subset directly using a logical vector, then supply this to
dba.count() using the
If you want a different subsets for multiple contrasts, you would need to create different DBA objects for each contrast.