Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.

Description

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.

Details

Author(s)

Lihua Julie Zhu, Jianhong Ou, Herve Pages, 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.
2. Y. Benjamini and D. Yekutieli (2001). The control of the false discovery rate in multiple hypothesis testing under dependency. Annals of Statistics. Accepted.
3. S. Durinck et al. (2005) BioMart and Bioconductor: a powerful link between biological biomarts and microarray data analysis. Bioinformatics, 21, 3439-3440.
4. S. Dudoit, J. P. Shaffer, and J. C. Boldrick (Submitted). Multiple hypothesis testing in microarray experiments.
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
6. Y. Hochberg (1988). A sharper Bonferroni procedure for multiple tests of significance, Biometrika. Vol. 75: 800-802.
7. S. Holm (1979). A simple sequentially rejective multiple test procedure. Scand. J. Statist.. Vol. 6: 65-70.
8. N. L. Johnson,S. Kotz and A. W. Kemp (1992) Univariate Discrete Distributions, Second Edition. New York: Wiley
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.

Examples

 if(interactive()){
  data(myPeakList)
  library(EnsDb.Hsapiens.v75)
  anno <- annoGR(EnsDb.Hsapiens.v75)
  annotatedPeak <- 
    annotatePeakInBatch(myPeakList[1:6], AnnotationData=anno)
 }

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ChIPpeakAnno)
Loading required package: grid
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: VennDiagram
Loading required package: futile.logger

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ChIPpeakAnno/ChIPpeakAnno-package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ChIPpeakAnno-package
> ### Title: Batch annotation of the peaks identified from either ChIP-seq or
> ###   ChIP-chip experiments.
> ### Aliases: ChIPpeakAnno-package ChIPpeakAnno
> ### Keywords: package
> 
> ### ** Examples
> 
> # if(interactive()){
>   data(myPeakList)
>   library(EnsDb.Hsapiens.v75)
Loading required package: ensembldb
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

>   anno <- annoGR(EnsDb.Hsapiens.v75)
>   annotatedPeak <- 
+     annotatePeakInBatch(myPeakList[1:6], AnnotationData=anno)
> # }
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>