findVennCounts {ChIPpeakAnno}R Documentation

Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram

Description

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

Usage

findVennCounts(Peaks, NameOfPeaks, maxgap = -1L, minoverlap = 0L,
               totalTest, useFeature=FALSE)

Arguments

Peaks

RangedDataList: See example below.

NameOfPeaks

Character vector to specify the name of Peaks, e.g., c("TF1", "TF2"), this will be used as label in the Venn Diagram.

maxgap,minoverlap

Used in the internal call to findOverlaps() to detect overlaps. See ?findOverlaps in the IRanges package for a description of these arguments.

totalTest

Numeric value to specify the total number of tests performed to obtain the list of peaks.

useFeature

TRUE or FALSE, default FALSE, true means using feature field in the RangedData for calculating overlap, false means using chromosome range for calculating overlap.

Value

p.value

hypergeometric testing result

vennCounts

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

Author(s)

Lihua Julie Zhu

See Also

makeVennDiagram


[Package ChIPpeakAnno version 3.14.2 Index]