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

Arguments

...

Objects of GRanges: See example below.

maxgap

Non-negative integer. Peak intervals with a separation of maxgap or less are considered to be overlapped.

minoverlap

Non-negative integer. Peak intervals with an overlapping of minoverlap or more are considered to be overlapped.

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.

Value

return value is An object of overlappingPeaks.
venn_cntan object of VennCounts
peaklista list consists of all overlapping peaks or unique peaks
overlappingPeaksa list of data frame consists of the annotation of all the overlapped peaks
all.peaksa list of GRanges object which contain the input peaks with formated rownames.

Details

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

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

Examples

Run this code

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

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