inclusive.overlap.internal: Internal inclusive overlap.
In ArnaudDroitLab/ef.utils: Eric Utilities

Returns the set of regions within all.regions where all conditions/proteins at indices which.factors are present, regardless of whether or not other factors are. Presence/absence at a given locus is obtained from the overlap.matrix parameter.

1	inclusive.overlap.internal(all.regions, overlap.matrix, which.factors)

`all.regions`	A GRanges object with the regions represented
`overlap.matrix`	A matrix, with rows corresponding to regions in `all.rgions`, and columns corresponding to proteins/factors. A non-zero value in the matrix indicates the protein/factor of interest is present at this region.
`which.factors`	Indices of columns where the factor should be present.