findOverlapsOfPeaks: Find the overlapped peaks among two or more set of peaks.
In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

Description Usage Arguments Details Value Author(s) References See Also Examples

Find the overlapping peaks for two or more (less than five) set of peak ranges.

findOverlapsOfPeaks(
  ...,
  maxgap = -1L,
  minoverlap = 0L,
  ignore.strand = TRUE,
  connectedPeaks = c("keepAll", "min", "merge")
)

`...`	Objects of GRanges: See example below.
`maxgap, minoverlap`	Used in the internal call to `findOverlaps()` to detect overlaps. See `?findOverlaps` in the IRanges package for a description of these arguments.
`ignore.strand`	When set to TRUE, the strand information is ignored in the overlap calculations.
`connectedPeaks`	If multiple peaks are involved in any group of connected/overlapping peaks in any input peak list, set it to "merge" will add 1 to the overlapping counts, while set it to "min" will add the minimal involved peaks in each group of connected/overlapped peaks to the overlapping counts. Set it to "keepAll" will add the number of involved peaks for each peak list to the corresponding overlapping counts. In addition, it will output counts as if connectedPeaks were set to "min". For examples (https://support.bioconductor.org/p/133486/#133603), if 5 peaks in group1 overlap with 2 peaks in group 2, setting connectedPeaks to "merge" will add 1 to the overlapping counts; setting it to "keepAll" will add 5 peaks to count.group1, 2 to count.group2, and 2 to counts; setting it to “min” will add 2 to the overlapping counts.

Efficiently perform overlap queries with an interval tree implemented with GRanges.

return value is An object of overlappingPeaks.

`venn_cnt`	an object of VennCounts
`peaklist`	a list consists of all overlapping peaks or unique peaks
`uniquePeaks`	an object of GRanges consists of all unique peaks
`mergedPeaks`	an object of GRanges consists of all merged overlapping peaks
`peaksInMergedPeaks`	an object of GRanges consists of all peaks in each samples involved in the overlapping peaks
`overlappingPeaks`	a list of data frame consists of the annotation of all the overlapped peaks
`all.peaks`	a list of GRanges object which contain the input peaks with formated rownames.

Jianhong Ou

1.Interval tree algorithm from: Cormen, Thomas H.; Leiserson, Charles E.; Rivest, Ronald L.; Stein, Clifford. Introduction to Algorithms, second edition, MIT Press and McGraw-Hill. ISBN 0-262-53196-8

2.Zhu L.J. et al. (2010) ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 2010, 11:237doi:10.1186/1471-2105-11-237

3. Zhu L (2013). "Integrative analysis of ChIP-chip and ChIP-seq dataset." In Lee T and Luk ACS (eds.), Tilling Arrays, volume 1067, chapter 4, pp. -19. Humana Press. http://dx.doi.org/10.1007/978-1-62703-607-8_8, http://link.springer.com/protocol/10.1007%2F978-1-62703-607-8_8

annotatePeakInBatch, makeVennDiagram, getVennCounts, findOverlappingPeaks

peaks1 <- GRanges(seqnames=c(6,6,6,6,5),
                 IRanges(start=c(1543200,1557200,1563000,1569800,167889600),
                         end=c(1555199,1560599,1565199,1573799,167893599),
                         names=c("p1","p2","p3","p4","p5")),
                 strand="+")
peaks2 <- GRanges(seqnames=c(6,6,6,6,5),
                  IRanges(start=c(1549800,1554400,1565000,1569400,167888600),
                          end=c(1550599,1560799,1565399,1571199,167888999),
                          names=c("f1","f2","f3","f4","f5")),
                  strand="+")
t1 <- findOverlapsOfPeaks(peaks1, peaks2, maxgap=1000)
makeVennDiagram(t1)
t1$venn_cnt
t1$peaklist