findOverlappingPeaks: Find the overlapping peaks for two peak ranges.

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 overlapping peaks for two peak ranges.

Description

Find the overlapping peaks for two input peak ranges.

Usage

findOverlappingPeaks(
  Peaks1,
  Peaks2,
  maxgap = -1L,
  minoverlap = 0L,
  multiple = c(TRUE, FALSE),
  NameOfPeaks1 = "TF1",
  NameOfPeaks2 = "TF2",
  select = c("all", "first", "last", "arbitrary"),
  annotate = 0,
  ignore.strand = TRUE,
  connectedPeaks = c("min", "merge"),
  ...
)

Arguments

Peaks1	GRanges: See example below.
Peaks2	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.
multiple	TRUE or FALSE: TRUE may return multiple overlapping peaks in Peaks2 for one peak in Peaks1; FALSE will return at most one overlapping peaks in Peaks2 for one peak in Peaks1. This parameter is kept for backward compatibility, please use select.
NameOfPeaks1	Name of the Peaks1, used for generating column name.
NameOfPeaks2	Name of the Peaks2, used for generating column name.
select	all may return multiple overlapping peaks, first will return the first overlapping peak, last will return the last overlapping peak and arbitrary will return one of the overlapping peaks.
annotate	Include overlapFeature and shortestDistance in the OverlappingPeaks or not. 1 means yes and 0 means no. Default to 0.
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 only 1, while set it to "min" will count it as the minimal involved peaks in any concered groups
...	Objects of GRanges: See also findOverlapsOfPeaks.

Details

The new function findOverlapsOfPeaks is recommended.

Efficiently perform overlap queries with an interval tree implemented in IRanges.

Value

OverlappingPeaks

a data frame consists of input peaks information with added information: overlapFeature (upstream: peak1 resides upstream of the peak2; downstream: peak1 resides downstream of the peak2; inside: peak1 resides inside the peak2 entirely; overlapStart: peak1 overlaps with the start of the peak2; overlapEnd: peak1 overlaps with the end of the peak2; includeFeature: peak1 include the peak2 entirely) and shortestDistance (shortest distance between the overlapping peaks)

MergedPeaks

GRanges contains merged overlapping peaks

Author(s)

Lihua Julie Zhu

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, 11:237 doi: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

See Also

findOverlapsOfPeaks, annotatePeakInBatch, makeVennDiagram

Examples

    if (interactive())
    {    
    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=as.integer(1))
    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=as.integer(1))
    t1 =findOverlappingPeaks(peaks1, peaks2, maxgap=1000, 
          NameOfPeaks1="TF1", NameOfPeaks2="TF2", select="all", annotate=1) 
    r = t1$OverlappingPeaks
    pie(table(r$overlapFeature))
    as.data.frame(t1$MergedPeaks)
    }

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.