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

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

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("keepAll", "min", "merge")
)

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. If 0 < minoverlap < 1, the function will find overlaps by percentage covered of interval and the filter condition will be set to max covered percentage of overlapping peaks.
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.

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
t2 <- findOverlapsOfPeaks(peaks1, peaks2, minoverlap = .5)
makeVennDiagram(t2)

t3 <- findOverlapsOfPeaks(peaks1, peaks2, minoverlap = .90)
makeVennDiagram(t3)

jianhong/ChIPpeakAnno documentation built on Feb. 2, 2024, 3:26 p.m.