oligoFrequency


    The sequences packaged in DNAStringSet, DNAString object or output of 
    function <a rd-options="" href="/link/getAllPeakSequence?package=ChIPpeakAnno&version=3.6.5" data-mini-rdoc="ChIPpeakAnno::getAllPeakSequence">getAllPeakSequence</a>.


sequence

MarkovOrder

last


 Prepare the oligonucleotide frequency for given Markov order. 


 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

oligoFrequency function


    The sequences packaged in DNAStringSet, DNAString object or output of 
    function <a rd-options='' href='getAllPeakSequence'>getAllPeakSequence</a>.


oligoFrequency: get the oligonucleotide frequency

Description

Usage

Arguments

Value

See Also

Examples