This function takes the regions found in calculatePvalues and assigns them genomic states contructed with makeGenomicState. The main workhorse functions are countOverlaps and findOverlaps.
A GRanges object created with makeGenomicState.
It can be either the
Arguments passed to other methods and/or advanced arguments. Advanced arguments:
Passed to extendedMapSeqlevels, countOverlaps and findOverlaps-methods.
You might want to specify arguments such as
minoverlap to control
how the overlaps are determined. See findOverlaps
for further details.
A list with elements
This is a data.frame with the number of overlaps from the
regions vs the genomic states with one type per column. For example, if
fullOrCoding='full' then the columns are
This is a
GRangesList with the genomic states
that overlapped with the regions. The
names of this
GRangesList correspond to the region index in
Andrew Jaffe, Leonardo Collado-Torres
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