findOverlapsOfPeaks

0th

Percentile

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

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

Keywords
misc
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.
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
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.

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

Aliases
  • findOverlapsOfPeaks
  • overlappingPeaks
  • overlappingPeaks-class
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
Documentation reproduced from package ChIPpeakAnno, version 3.6.5, License: GPL (>= 2)

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