R语言 REDseq包 REDseq-package()函数中文帮助文档(中英文对照)

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REDseq-package(REDseq)
REDseq-package()所属R语言包：REDseq

                                         REDseq
                                         REDseq

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

REDSeq is a Bioconductor package for building genomic map of restriction enzyme sites REmap, assigning sequencing tags to RE sites using five different strategies, visualizing genome-wide distribution of differentially cut regions with the REmap as reference and the distance distribution of sequence tags to corresponding RE sites, generating count table for identifying statistically significant RE sites using edgeR or DEseq.
REDSeq是一个用于构建基因组图谱，限制性内切酶的网站重新映射分配序列标签重新使用五个不同的策略的网站，作为参考序列标签的距离分布到相应的再重映射与可视化的全基因组分布区域差异削减Bioconductor包网站，使用磨边或DEseq确定统计学意义重点为伯爵表。


Details

详情----------Details----------

~~ An overview of how to use the package, including the most important functions ~~
~概述如何使用包，其中包括最重要的功能~~


作者（S）----------Author(s)----------



Lihua Julie Zhu

Maintainer:  
Lihua Julie Zhu <julie.zhu@umassmed.edu>




参考文献----------References----------

2. Kessler, C. and V. Manta, Specificity of restriction endonucleases and DNA modification methyltransferases a review (Edition 3). Gene, 1990. 92(1-2): p. 1-248. <br> 3. Pingoud, A., J. Alves, and R. Geiger, Restriction enzymes. Methods Mol Biol, 1993. 16: p. 107-200. <br> 4. Anders, S. and W. Huber, Differential expression analysis for sequence count data. Genome Biol, 2010. 11(10): p. R106. <br> 5. Robinson, M.D., D.J. McCarthy, and G.K. Smyth, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 2010. 26(1): p. 139-40. <br> 6. Zhu, L.J., et al., ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics, 2010. 11: p. 237. <br> 7. Pages, H., BSgenome package. http://bioconductor.org/packages/2.8/bioc/<br> vignettes/BSgenome/inst/doc/GenomeSearching.pdf <br> 8. Zhu, L.J., et al., REDseq: A Bioconductor package for Analyzing High Throughput Sequencing Data from Restriction Enzyme Digestion. (In preparation) <br>

参见----------See Also----------

buildREmap, assignSeq2REsit, plotCutDistribution, distanceHistSeq2RE, summarizeByRE, summarizeBySeq, compareREseq, binom.test.REDseq
buildREmap，assignSeq2REsit，plotCutDistribution，distanceHistSeq2RE，summarizeByRE，summarizeBySeq，compareREseq，binom.test.REDseq


举例----------Examples----------


        if(interactive()){
        library(ChIPpeakAnno)
        REpatternFilePath = system.file("extdata", "examplePattern.fa", package="REDseq")
        library(BSgenome.Celegans.UCSC.ce2)
        buildREmap( REpatternFilePath, BSgenomeName=Celegans, outfile=tempfile())
        library(REDseq)
        data(example.REDseq)
        data(example.map)
        r.unique = assignSeq2REsite(example.REDseq, example.map, cut.offset = 1,
seq.length = 36, allowed.offset = 5, min.FragmentLength = 60,
max.FragmentLength = 300, partitionMultipleRE = "unique")
        r.average = assignSeq2REsite(example.REDseq, example.map, cut.offset = 1,
seq.length = 36, allowed.offset = 5, min.FragmentLength = 60,
max.FragmentLength = 300, partitionMultipleRE = "average")
        r.random = assignSeq2REsite(example.REDseq, example.map, cut.offset = 1,
seq.length = 36, allowed.offset = 5, min.FragmentLength = 60,
max.FragmentLength = 300, partitionMultipleRE = "random")
        r.best = assignSeq2REsite(example.REDseq, example.map, cut.offset = 1,
seq.length = 36, allowed.offset = 5, min.FragmentLength = 60,
max.FragmentLength = 300, partitionMultipleRE = "best")
        r.estimate = assignSeq2REsite(example.REDseq, example.map, cut.offset = 1,
seq.length = 36, allowed.offset = 5, min.FragmentLength = 60,
max.FragmentLength = 300, partitionMultipleRE = "estimate")
        r.estimate$passed.filter
        r.estimate$notpassed.filter
        data(example.assignedREDseq)
        plotCutDistribution(example.assignedREDseq,example.map,
chr="2", xlim =c(3012000, 3020000))
        distanceHistSeq2RE(example.assignedREDseq,ylim=c(0,20))
        summarizeByRE(example.assignedREDseq,by="Weight",sampleName="example")
        REsummary  =summarizeByRE(example.assignedREDseq,by="Weight")
        binom.test.REDseq(REsummary)
}

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


注：
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