ChIPpeakAnno (version 3.6.5)

findOverlappingPeaks: Find the overlapping peaks for two peak ranges.

Description

Find the overlapping peaks for two input peak ranges.

This function is to keep the backward compatibility with previous versions for RangedData object.

The new function findOverlapsOfPeaks is recommended.

Convert RangedData to GRanges with toGRanges function.

Usage

findOverlappingPeaks(Peaks1, Peaks2, maxgap = 0L, minoverlap=1L, 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

RangedData: See example below.

Peaks2

RangedData: See example below.

maxgap

Non-negative integer. Intervals with a separation of maxgap or less are considered to be overlapping.

minoverlap

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

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 or RangedData: See also findOverlapsOfPeaks.

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

RangedData contains merged overlapping peaks

Details

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

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 = 
        RangedData(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),space=c(6,6,6,6,5))
    peaks2 = 
        RangedData(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),space=c(6,6,6,6,5))
    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)
    }