Non-negative integer. Intervals with a separation of maxgap or
less are considered to be overlapping.
minoverlap
Non-negative integer. Intervals with an overlapping of
minoverlap or more are considered to be overlapping.
multiple
TRUE or FALSE: TRUE may return multiple overlapping peaks in
Peaks2 for one peak in Peaks1; FALSE will return at most one overlapping
peaks in Peaks2 for one peak in Peaks1. This parameter is kept for backward
compatibility, please use select.
NameOfPeaks1
Name of the Peaks1, used for generating column name.
NameOfPeaks2
Name of the Peaks2, used for generating column name.
select
all may return multiple overlapping peaks, first will return
the first overlapping peak, last will return the last overlapping peak and
arbitrary will return one of the overlapping peaks.
annotate
Include overlapFeature and shortestDistance in the OverlappingPeaks or not.
1 means yes and 0 means no. Default to 0.
ignore.strand
When set to TRUE, the strand information is ignored in the overlap
calculations.
connectedPeaks
If multiple peaks involved in overlapping in several groups, set it to
"merge" will count it as only 1, while set it to "min" will count it as
the minimal involved peaks in any concered groups
...
Objects of GRanges or
RangedData: See also
findOverlapsOfPeaks.
Or any parameter need to be passed into read.delim function for
2RangedData function.
header
TRUE or FALSE, default to FALSE,
indicates whether data file has header
data.BED
BED format data frame or BED filename,
please refer to http://genome.ucsc.edu/FAQ/FAQformat#format1 for details
data.GFF
GFF format data frame or GFF file name,
please refer to http://genome.ucsc.edu/FAQ/FAQformat#format3 for details
Details
findOverlappingPeaks is now deprecated wrappers for
findOverlapsOfPeaks
providing 
.