ChIPpeakAnno (version 3.4.0)

makeVennDiagram: Make Venn Diagram from a list of peaks

Description

Make Venn Diagram from two or more peak ranges, Also calculate p-value to determine whether those peaks overlap significantly.

Usage

makeVennDiagram(Peaks, NameOfPeaks, maxgap = 0L, minoverlap = 1L, totalTest, by = c("region", "feature", "base"), ignore.strand = TRUE, connectedPeaks = c("min", "merge", "keepAll"), method = c("hyperG", "permutation"), TxDb, ...)

Arguments

Peaks

A list of peaks in GRanges format: 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. It should be much larger than the number of peaks in the largest peak set.

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 calculating overlap in nucleotide level.

ignore.strand

Logical: 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 connected peak group.

method

method used for p value calculation. hyperG means hypergeometric test and permutation means peakPermTest

TxDb

An object of TxDb

...

Additional arguments to be passed to venn.diagram

Value

In addition to a Venn Diagram produced, a p.value is calculated by hypergeometric test to determine whether the peaks or features are overlapped significantly.

Details

For customized graph options, please see venn.diagram in VennDiagram package.

See Also

findOverlapsOfPeaks, venn.diagram, peakPermTest

Examples

if (interactive()){
    peaks1 <- GRanges(seqnames=c("1", "2", "3"),
                      IRanges(start=c(967654, 2010897, 2496704),
                              end=c(967754, 2010997, 2496804), 
                              names=c("Site1", "Site2", "Site3")),
                      strand="+",
                      feature=c("a","b","f"))
    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("+", "+", "-", "-", "+"), 
                        feature=c("a","b","c","d","a"))
    makeVennDiagram(list(peaks1, peaks2), NameOfPeaks=c("TF1", "TF2"),
                    totalTest=100,scaled=FALSE, euler.d=FALSE)
    
    makeVennDiagram(list(peaks1, peaks2), NameOfPeaks=c("TF1", "TF2"),
                    totalTest=100)
    
    ###### 4-way diagram using annotated feature instead of chromosome ranges
    
    makeVennDiagram(list(peaks1, peaks2, peaks1, peaks2), 
                    NameOfPeaks=c("TF1", "TF2","TF3", "TF4"), 
                    totalTest=100, by="feature",
                    main = "Venn Diagram for 4 peak lists",
                    fill=c(1,2,3,4))
}

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