ChIPpeakAnno (version 3.6.5)

getVennCounts: Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram

Description

Obtain Venn Counts for peak ranges using chromosome ranges or feature field, internal function for makeVennDigram

Usage

getVennCounts(..., maxgap = 0L, minoverlap=1L,  by=c("region", "feature", "base"),  ignore.strand=TRUE, connectedPeaks=c("min", "merge", "keepAll"))

Arguments

...

Objects of GRanges or 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.

by

region, feature or base, default region. feature means using feature field in the RangedData or GRanges for calculating overlap, region means using chromosome range for calculating overlap, and base means using calculating overlap in nucleotide level.

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

Value

vennCounts

vennCounts objects containing counts for Venn Diagram generation, see details in limma package vennCounts

See Also

makeVennDiagram, findOverlappingPeaks

Examples

if(interactive()){
peaks1 = RangedData(IRanges(start = c(967654, 2010897, 2496704), 
                            end = c(967754, 2010997, 2496804), 
                            names = c("Site1", "Site2", "Site3")), 
                   space = c("1", "2", "3"), 
                   strand=as.integer(1), 
                   feature=c("a","b", "c"))
  peaks2 = 
      RangedData(IRanges(start=c(967659, 2010898, 2496700, 3075866, 3123260), 
                         end=c(967869, 2011108, 2496920, 3076166, 3123470), 
                         names = c("t1", "t2", "t3", "t4", "t5")), 
                    space = c("1", "2", "3", "1", "2"), 
                    strand = c(1, 1, -1,-1,1), 
                    feature=c("a","c","d","e", "a"))
    getVennCounts(peaks1,peaks2, maxgap=0)
    getVennCounts(peaks1,peaks2, maxgap=0, by="feature")
    getVennCounts(peaks1, peaks2, maxgap=0, by="base")
}