permPool

permPool-class

permPool-method

$,permPool-method

$<-,permPool-method


  An object of class <code>"permPool"</code> represents the possible locations to do
  permutation test.


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

permPool-class function

Objects can be created by calls of the form 
  <code>new("permPool", grs="GRangesList", N="integer")</code>.

Objects from the Class

<dl>
    <dt><code>grs</code></dt><dd>
    object of <code>"GRangesList"</code> The list of binding ranges</dd> <dt><code>N</code></dt><dd>
    vector of <code>"integer"</code>, permutation number for each ranges</dd> </dl> 

Slots

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

permPool-class: Class `"permPool"`

Description

Arguments

Objects from the Class

Slots

Methods

See Also