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

Class <code>"permPool"</code>

permPool-class: Class `"permPool"`

Description

Arguments

Objects from the Class

See Also