bindist

bindist-class

bindist-method

$,bindist-method

$<-,bindist-method


  An object of class <code>"bindist"</code> represents the relevant fixed-width range
  of binding site from the feature and number of possible binding site 
  in each range.


classes

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

bindist-class function

Objects can be created by calls of the form 
  <code>new("bindist", counts="integer",
                            mids="integer",
                            halfBinSize="integer",
                            bindingType="character",
                            featureType="character")</code>.

Objects from the Class

<dl>
    <dt><code>counts</code></dt><dd>
        vector of <code>"integer"</code> The count number in each binding range
    </dd> <dt><code>mids</code></dt><dd>
        vector of <code>"integer"</code> The center of each range relevant to feature
    </dd> <dt><code>halfBinSize</code></dt><dd>
        <code>"integer"</code>, length must be 1. 
        the fixed half-width of each binding range
    </dd> <dt><code>bindingType</code></dt><dd>
        a <code>"character"</code>. could be "TSS", "geneEnd"
    </dd> <dt><code>featureType</code></dt><dd>
        a <code>"character"</code>. could be "transcript", "exon"
    </dd> </dl> 

Slots

<dl>
    <dt>$, $&lt;-</dt><dd>Get or set the slot of <code><a rd-options="" href="/link/bindist?package=ChIPpeakAnno&version=3.6.5" data-mini-rdoc="ChIPpeakAnno::bindist">bindist</a></code></dd> </dl> 

bindist-class: Class `"bindist"`

Description

Arguments

Objects from the Class

Slots

Methods

See Also