spliceVariants(edgeR)
spliceVariants()所属R语言包：edgeR
Identify Genes with Splice Variants
识别与剪接变异体的基因
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Identify genes exhibiting evidence for splice variants (alternative exon usage/transcript isoforms) from exon-level count data using negative binomial generalized linear models.
识别参展证据剪接变异体，从外显子级计数数据使用负二项式的广义线性模型（使用替代外显子/成绩单亚型）的基因。
用法----------Usage----------
spliceVariants(y, geneID, dispersion=NULL, group=NULL, estimate.genewise.disp=TRUE, trace=FALSE)
参数----------Arguments----------
参数：y
either a matrix of exon-level counts or a DGEList object with (at least) elements counts (table of counts summarized at the exon level) and samples (data frame containing information about experimental group, library size and normalization factor for the library size). Each row of y should represent one exon.
无论是外显子级计数矩阵或DGEList（至少）元素的对象counts（外显子水平在总结数表）和samples（数据框包含的信息，有关实验组，库的大小和规范化因子库的大小）。每个y行应该代表一个外显子。
参数：geneID
vector of length equal to the number of rows of y, which provides the gene identifier for each exon in y. These identifiers are used to group the relevant exons into genes for the gene-level analysis of splice variation.
矢量长度y，它提供了每个y的外显子基因标识的行数相等的。这些标识符用于分组到有关的外显子剪接变异基因水平分析基因。
参数：dispersion
scalar (in future a vector will also be allowed) supplying the negative binomial dispersion parameter to be used in the negative binomial generalized linear model.
标量（也将被允许在未来的一个向量）提供负二项分布负二项式的广义线性模型中使用的分散参数。
参数：group
factor supplying the experimental group/condition to which each sample (column of y) belongs. If NULL (default) the function will try to extract if from y, which only works if y is a DGEList object.
因素提供实验组/条件，每个样品属于（y列）。如果NULL（默认）函数将尝试提取如果从y，这只是如果y是DGEList对象。
参数：estimate.genewise.disp
logical, should genewise dispersions (as opposed to a common dispersion value) be computed if the dispersion argument is NULL?
逻辑，应该2-6。分散（而不是一个普通的色散值）计算，如果dispersion参数是NULL？
参数：trace
logical, whether or not verbose comments should be printed as function is run. Default is FALSE.
逻辑详细的意见，不论是否应打印功能运行。默认FALSE。
Details
详情----------Details----------
This function can be used to identify genes showing evidence of splice variation (i.e. alternative splicing, alternative exon usage, transcript isoforms). A negative binomial generalized linear model is used to assess evidence, for each gene, given the counts for the exons for each gene, by fitting a model with an interaction between exon and experimental group and comparing this model (using a likelihood ratio test) to a null model which does not contain the interaction. Genes that show significant evidence for an interaction between exon and experimental group by definition show evidence for splice variation, as this indicates that the observed differences between the exon counts between the different experimental groups cannot be explained by consistent differential expression of the gene across all exons. The function topTags can be used to display the results of spliceVariants with genes ranked by evidence for splice variation.
此功能可用于识别剪接的证据显示变异（即剪接，替代使用外显子，转录异构体）的基因。负二项式的广义线性模型，用于评估证据，对每一个基因，每个基因的外显子数，外显子和实验组之间的相互作用与拟合模型，并比较模型（用似然比检验）一个空的模式，不包含互动。基因，表明外显子和定义剪接变异显示的证据，实验组之间的相互作用的显著证据作为这表明跨所有外显子的基因一致的差分表达的不同实验组之间的外显子数之间的观测差异不能解释。的功能topTags可以用来显示spliceVariants基因剪接变异的证据排名结果。
值----------Value----------
spliceVariants returns a DGEExact object, which contains a table of results for the test of differential splicing between experimental groups (alternative exon usage), a data frame containing the gene identifiers for which results were obtained and the dispersion estimate(s) used in the statistical models and testing.
spliceVariants返回一个DGEExact对象，其中包含一个实验组（替代外显子的用法），结果获得含有基因标识一个数据框和分散之间的差拼接测试结果表估计（S）在统计模型和测试使用。
作者（S）----------Author(s)----------
Davis McCarthy, Gordon Smyth
参见----------See Also----------
estimateExonGenewiseDisp for more information about estimating genewise dispersion values from exon-level counts. DGEList for more information about the DGEList class. topTags for more information on displaying ranked results from spliceVariants. estimateCommonDisp and related functions for estimating the dispersion parameter for the negative binomial model.
estimateExonGenewiseDisp为2-6。色散值估计从外显子级计数的详细信息。 DGEListDGEList类的更多信息。 topTags排名结果显示，从spliceVariants的更多信息。 estimateCommonDisp和色散为负二项分布模型参数估计的相关职能。
举例----------Examples----------
# generate exon counts from NB, create list object[来自NB产生外显子数，创建列表对象]
y<-matrix(rnbinom(40,size=1,mu=10),nrow=10)
d<-DGEList(counts=y,group=rep(1:2,each=2))
genes <- rep(c("gene.1","gene.2"), each=5)
disp <- 0.2
spliceVariants(d, genes, disp)
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 17:10:05
