ChIPpeakAnno (version 2.16.4)

makeVennDiagram: Make Venn Diagram from two peak ranges

Description

Make Venn Diagram from two peak ranges and also calculate p-value for determining whether two peak ranges overlap significantly.

Usage

makeVennDiagram(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. It should be much larger than the number of peaks in the largest peak set.

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.

...

Additional arguments to be passed to venn.diagram

Value

In addition to a Venn Diagram produced, p.value is obtained from hypergeometric test for determining whether the two peak ranges or features overlap significantly.

Details

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

References

See Also

findOverlappingPeaks, venn.diagram

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","f"))
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","b","c","d","a"))
makeVennDiagram(RangedDataList(peaks1,peaks2), NameOfPeaks=c("TF1", "TF2"),
 totalTest=100,scaled=F, euler.d=F)

makeVennDiagram(RangedDataList(peaks1,peaks2), NameOfPeaks=c("TF1", "TF2"),
  totalTest=100,useFeature=FALSE)

###### 4-way diagram using annotated feature instead of chromosome ranges

	makeVennDiagram(RangedDataList(peaks1,peaks2, peaks1, peaks2), NameOfPeaks=c("TF1", "TF2","TF3", "TF4"), totalTest=100,useFeature=TRUE,
main = "Venn Diagram for 4 peak lists",fill=c(1,2,3,4))
}