getVennCounts

0th

Percentile

Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram

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

Keywords
misc
Usage
getVennCounts(..., maxgap = 0L, minoverlap=1L, by=c("region", "feature", "base"), ignore.strand=TRUE, connectedPeaks=c("min", "merge", "keepAll"))
Arguments
...
Objects of GRanges or RangedData: See example below.
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.
by
region, feature or base, default region. feature means using feature field in the RangedData or 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

See Also

makeVennDiagram, findOverlappingPeaks

Aliases
  • getVennCounts
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", "c"))
  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","c","d","e", "a"))
    getVennCounts(peaks1,peaks2, maxgap=0)
    getVennCounts(peaks1,peaks2, maxgap=0, by="feature")
    getVennCounts(peaks1, peaks2, maxgap=0, by="base")
}
Documentation reproduced from package ChIPpeakAnno, version 3.6.5, License: GPL (>= 2)

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