myPeakList


 the putative STAT1-binding regions identified in un-stimulated cells using 
 ChIP-seq technology (Robertson et al., 2007) 


datasets

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

myPeakList function

GRanges with slot rownames containing the ID of peak as character, slot start
  containing the start position of the peak, slot end containing the end 
  position of the peak and seqnames containing the chromosome where the peak 
  is located.

Format

Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, et al. (2007) 
  Genome-wide profiles of STAT1 DNA association using chromatin 
  immunoprecipitation and massively parallel sequencing. Nat Methods 4:651-7

myPeakList: An example GRanges object representing a ChIP-seq peak dataset

Description

Usage

Arguments

Format

Source

Examples