ChIPpeakAnno-package(ChIPpeakAnno)
ChIPpeakAnno-package()所属R语言包：ChIPpeakAnno
Batch annotation of the peaks identified from either ChIP-seq or ChIP-chip experiments.
无论从芯片SEQ芯片的芯片实验确定峰批次标注。
译者：生物统计家园网 机器人LoveR
描述----------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.
该软件包包括函数来检索峰值周围的序列，获得丰富的基因本体（GO）的条款，找到最近的基因，外显子的miRNA或利用biomaRt最保守的元素和其他转录因子结合位点，IRanges，Biostrings如自定义功能， BSgenome，GO.db，超几何的测试phyper和multtest包。
Details
详情----------Details----------
作者（S）----------Author(s)----------
Lihua Julie Zhu, Herve Pages, Claude Gazin, Nathan Lawson, Simon Lin, David Lapointe and Michael Green
Maintainer:
Lihua Julie Zhu <julie.zhu@umassmed.edu>
参考文献----------References----------
2. Y. Benjamini and D. Yekutieli (2001). The control of the false discovery rate in multiple hypothesis testing under dependency. Annals of Statistics. Accepted. <br> 3. S. Durinck et al. (2005) BioMart and Bioconductor: a powerful link between biological biomarts and microarray data analysis. Bioinformatics, 21, 3439-3440. <br> 4. S. Dudoit, J. P. Shaffer, and J. C. Boldrick (Submitted). Multiple hypothesis testing in microarray experiments. <br> 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 <br> 6. Y. Hochberg (1988). A sharper Bonferroni procedure for multiple tests of significance, Biometrika. Vol. 75: 800-802. <br> 7. S. Holm (1979). A simple sequentially rejective multiple test procedure. Scand. J. Statist.. Vol. 6: 65-70. <br> 8. N. L. Johnson,S. Kotz and A. W. Kemp (1992) Univariate Discrete Distributions, Second Edition. New York: Wiley <br> 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.<br>
参见----------See Also----------
getAnnotation, annotatePeakInBatch, getAllPeakSequence, write2FASTA, convert2EntrezID, addAncestors, getEnrichedGO,BED2RangedData, GFF2RangedData, makeVennDiagram,findOverlappingPeaks, addGeneIDs, peaksNearBDP,summarizePatternInPeaks)
getAnnotation，annotatePeakInBatch，getAllPeakSequence，write2FASTA，convert2EntrezID，addAncestors，getEnrichedGO，BED2RangedData，GFF2RangedData，makeVennDiagram，findOverlappingPeaks，addGeneIDs，peaksNearBDP，summarizePatternInPeaks）
举例----------Examples----------
if (interactive())
{
data(myPeakList)
data(TSS.human.NCBI36)
myPeakList1 = myPeakList[1:6,]
annotatedPeak = annotatePeakInBatch(myPeakList1, AnnotationData=TSS.human.NCBI36)
peaks = RangedData(IRanges(start=c(100, 500), end=c(300, 600),
names=c("peak1", "peak2")), space=c("NC_008253", "NC_010468"))
library(BSgenome.Ecoli.NCBI.20080805)
peaksWithSequences = getAllPeakSequence(peaks, upstream = 20,
downstream = 20, genome = Ecoli)
write2FASTA(peaksWithSequences, file="testseq.fasta", width=50)
filepath =system.file("extdata", "examplePattern.fa", package="ChIPpeakAnno")
summarizePatternInPeaks(patternFilePath=filepath, format="fasta", skip=0L, BSgenomeName=Ecoli, peaks=peaks)
library(org.Hs.eg.db)
annotatedPeak.withSymbol =addGeneIDs(annotatedPeak,"org.Hs.eg.db",c("symbol"))
enrichedGO = getEnrichedGO(annotatedPeak, orgAnn ="org.Hs.eg.db", maxP=0.01,
multiAdj=FALSE, minGOterm=10, multiAdjMethod="")
enriched.biologicalprocess = enrichedGO$bp
enriched.molecularfunction = enrichedGO$mf
enriched.cellularcomponent = enrichedGO$cc
data(annotatedPeak)
y = annotatedPeak$distancetoFeature[!is.na(annotatedPeak$distancetoFeature)]
hist(y, xlab="Distance To Nearest TSS", main="", breaks=1000,
xlim=c(min(y)-100, max(y)+100))
annotatedBDP = peaksNearBDP(myPeakList1, AnnotationData=TSS.human.NCBI36,
MaxDistance=5000,PeakLocForDistance = "middle", FeatureLocForDistance = "TSS")
c(annotatedBDP$percentPeaksWithBDP, annotatedBDP$n.peaks, annotatedBDP$n.peaksWithBDP)
}
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-25 14:47:51
