findOverlapsOfPeaks: Find the overlapped peaks among two or more set of peaks.
In LihuaJulieZhu/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 involved in overlapping in several groups, set it to "merge" will count it as 1, while set it to "min" will count it as the minimal involved peaks in any group of connected/overlapped peaks. "keepAll" will keep all the orginal counts for each list while the final counts will be same as "min".

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