findOverlapsOfPeaks {ChIPpeakAnno} | R Documentation

## Find the overlapped peaks among two or more set of peaks.

### Description

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

### Usage

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

### Arguments

`...` | 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.

### Details

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

### Value

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.

### Author(s)

Jianhong Ou

### References

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

### See Also

annotatePeakInBatch, makeVennDiagram, getVennCounts, findOverlappingPeaks

### Examples

    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

[Package ChIPpeakAnno version 3.12.7 Index]