R/ChIPpeakAnno.R

In ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges

#' Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip
#' experiments.
#' 
#' 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 leveraging biomaRt, IRanges, Biostrings, BSgenome,
#' GO.db, hypergeometric test phyper and multtest package.
#' 
#' \tabular{ll}{ Package: \tab ChIPpeakAnno\cr Type: \tab Package\cr Version:
#' \tab 3.0.0\cr Date: \tab 2014-10-24\cr License: \tab LGPL\cr LazyLoad: \tab
#' yes\cr }
#' 
#' @name ChIPpeakAnno-package
#' @aliases ChIPpeakAnno-package ChIPpeakAnno
#' @docType package
#' @author Lihua Julie Zhu, Jianhong Ou, Hervé Pagès, Claude Gazin, Nathan
#' Lawson, Simon Lin, David Lapointe and Michael Green
#' 
#' Maintainer: Jianhong Ou <jianhong.ou@@umassmed.edu>, Lihua Julie Zhu
#' <julie.zhu@@umassmed.edu>
#' @references 1. Y. Benjamini and Y. Hochberg (1995). Controlling the false
#' discovery rate: a practical and powerful approach to multiple testing. J. R.
#' Statist. Soc. B. Vol. 57: 289-300. \cr 2. Y. Benjamini and D. Yekutieli
#' (2001). The control of the false discovery rate in multiple hypothesis
#' testing under dependency. Annals of Statistics. Accepted. \cr 3.  S. Durinck
#' et al. (2005) BioMart and Bioconductor: a powerful link between biological
#' biomarts and microarray data analysis. Bioinformatics, 21, 3439-3440. \cr 4.
#' S. Dudoit, J. P. Shaffer, and J. C. Boldrick (Submitted). Multiple
#' hypothesis testing in microarray experiments. \cr 5. Y. Ge, S. Dudoit, and
#' T. P. Speed. Resampling-based multiple testing for microarray data
#' hypothesis, Technical Report #633 of UCB Stat.
#' http://www.stat.berkeley.edu/~gyc \cr 6. Y. Hochberg (1988). A sharper
#' Bonferroni procedure for multiple tests of significance, Biometrika. Vol.
#' 75: 800-802. \cr 7. S. Holm (1979). A simple sequentially rejective multiple
#' test procedure. Scand. J. Statist.. Vol. 6: 65-70. \cr 8. N. L. Johnson,S.
#' Kotz and A. W. Kemp (1992) Univariate Discrete Distributions, Second
#' Edition. New York: Wiley \cr 9. Zhu L.J. et al. (2010) ChIPpeakAnno: a
#' Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC
#' Bioinformatics 2010, 11:237doi:10.1186/1471-2105-11-237.\cr
#' @keywords package
#' @examples
#' 
#'  if(interactive()){
#'   data(myPeakList)
#'   library(ensembldb)
#'   library(EnsDb.Hsapiens.v75)
#'   anno <- annoGR(EnsDb.Hsapiens.v75)
#'   annotatedPeak <-
#'     annotatePeakInBatch(myPeakList[1:6], AnnotationData=anno)
#'  }
#' 
"_PACKAGE"