getVennCounts {ChIPpeakAnno} | R Documentation

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

### 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.
`by` | region, feature or base, default region. feature means using feature field in the 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

### Author(s)

Jianhong Ou

### See Also

makeVennDiagram, findOverlappingPeaks

### Examples

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

[Package ChIPpeakAnno version 3.24.2 Index]