exonStructure(GeneRegionScan)
exonStructure()所属R语言包：GeneRegionScan
Add exon-structure to plots
外显子结构图
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function that will paint the exon structure of a gene on the plots obtained by plotOnGene.
功能，将画上一个基因的外显子结构由plotOnGene获得图。
用法----------Usage----------
exonStructure(mrna, genome, maxMismatch=4, y=0)
参数----------Arguments----------
参数：mrna
A gene sequence formatted as DNAstring, character-vectors or readFASTA output.
A基因序列的DNAstring，字符矢量或readFASTA输出的格式为。
参数：genome
A number of gene sequences as DNAstring, vectors of DNAStrings, character-vectors or readFASTA outputs.
一个号码作为DNAstring基因序列，向量DNAStrings，字符矢量或readFASTA输出的。
参数：maxMismatch
Integer. The maximum number of mismatches per exon that can be allowed before the exon is not allocated at the position in the template mrna. Defaults to 4.
整数。每个外显子的不匹配外显子前，可以允许的最大数量是未分配的模板mRNA的位置。默认值为4。
参数：y
Numeric. The vertical position of the exon structure (if ylim is changed)
数字。外显子结构的垂直位置（如果改变ylim）
Details
详情----------Details----------
When given a sequence of the DNA divided by exons and a sequence of the corresponding mRNA string, this function will plot the layout of exons along the length of the x-axis on the current device. The sequences have to be given as FASTA sequences produced by the readFASTA function in the Biostrings package. Furthermore the genome must be divided with an entry for each exon. This is easily done by downloading the genome sequences of the gene-of-interest from http://genome.ucsc.edu and specifying "One FASTA record per region".
当给定一个除以外显子和相应的mRNA的字符串序列的DNA序列，此功能将绘制当前设备上的X-轴的长度沿外显子的布局。序列必须由在Biostrings包readFASTA功能产生的FASTA格式序列。此外，基因组中必须划分为每个外显子的条目。这是很容易做到的基因组序列的基因利益从http://genome.ucsc.edu下载，并指定“每一个区域FASTA格式纪录”。
The function works by sequentially comparing each exon to the mrna. The location of the match start and end is taken as the exon boundaries and plotted. If more than one match is found a warning is given. If no match is found for an exon this is printed, but otherwise ignored. The mrna can in fact also be DNA sequence with introns. The important thing is that it serves as template for the exon matching.
该函数的工作原理是依次比较每个外显子的mRNA。比赛的起点和终点的位置，便被视为外显子的边界，并绘制。如果发现多个匹配，给予警告。如果没有匹配的外显子中发现，这是印刷，但另有忽略。 mRNA的其实也可以是DNA序列与内含子。重要的是，它作为外显子匹配的模板。
Importantly, the exon-numbers technically refer to "number of exon in investigated transcript". For example if an DNA with exon structure for an isoform which does not include all exons in the gene is investigated, then there will be skips of exon numbers. To avoid this, the DNA for an isoform which do include all exons could be used. However, it is really more a biological issue: different sources can differ on where to start the counting for a given gene in any case.
重要的是，外显子数技术上是指以“号外显子在调查谈话”。例如，如果一个外显子，其中不包括在基因所有外显子的亚型结构的DNA研究，那么将跳过外显子的数字。为了避免这种情况，哪一个亚型的DNA，包括可用于所有外显子。然而，它是真的，一个生物问题：不同的来源可以从哪里开始计数，在任何情况下的特定基因不同。
值----------Value----------
No value, but plots the layout of exons in a gene on the product of a call to plotOnGene.
没有价值，但图外显子在基因上调用plotOnGene产品布局。
作者（S）----------Author(s)----------
Lasse Folkersen
参见----------See Also----------
geneRegionScan, plotOnGene
geneRegionScan，plotOnGene
举例----------Examples----------
data(exampleProbeLevelSet)
plotOnGene(exampleProbeLevelSet, mrna, label="gender", testType="wilcoxon")
exonStructure(mrna, genomic, maxMismatch=2)
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 18:57:50
