ChIPpeakAnno (version 3.6.5)

findVennCounts: 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 = 0L, minoverlap = 1L, 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
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.
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

See Also

makeVennDiagram