findVennCounts

Peaks

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

NameOfPeaks

Non-negative integer. Intervals with a separation of maxgap or less are 
 considered to be overlapping.

maxgap

Non-negative integer. Intervals with an overlapping of minoverlap or more are 
considered to be overlapping.

minoverlap

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

totalTest

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

useFeature

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

misc

The package includes functions to retrieve the sequences
    around the peak, obtain enriched Gene Ontology (GO) terms, find
    the nearest gene, exon, miRNA or custom features such as most
    conserved elements and other transcription factor binding sites
    supplied by users. Starting 2.0.5, new functions have been
    added for finding the peaks with bi-directional promoters with
    summary statistics (peaksNearBDP), for summarizing the
    occurrence of motifs in peaks (summarizePatternInPeaks) and for
    adding other IDs to annotated peaks or enrichedGO (addGeneIDs).
    This package leverages the biomaRt, IRanges, Biostrings,
    BSgenome, GO.db, multtest and stat packages.

Lihua Julie Zhu

ChIPpeakAnno

Batch annotation of the peaks identified from either ChIP-seq,
    ChIP-chip experiments or any experiments resulted in large
    number of chromosome ranges

findVennCounts function

Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram

p.value

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

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findVennCounts: Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram

Description

Usage

Arguments

Value

See Also