R语言 VanillaICE包 gtEmission()函数中文帮助文档(中英文对照)

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gtEmission(VanillaICE)
gtEmission()所属R语言包：VanillaICE

                                        Calculate emission probabilities for genotypes
                                         发射概率计算基因型

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Calculate emission probabilities for genotypes diallelic genotypes.
发射概率计算为diallelic基因型基因型。


用法----------Usage----------


gtEmission(object, hmm.params, gt.conf, is.snp, cdfName, ...)



参数----------Arguments----------

参数：object
A object of class SnpSet, oligoSnpSet, or matrix.  
一个对象的类SnpSet，oligoSnpSet或matrix。


参数：hmm.params
A HmmOptionList.  
AHmmOptionList。


参数：gt.conf
Ignored unless object is of class matrix.
被忽略，除非对象类matrix。


参数：is.snp
Ignored unless object is of class matrix.
被忽略，除非对象类matrix。


参数：cdfName
Ignored unless the argument ICE for the HmmOptionList object is TRUE.
被忽略，除非参数ICEHmmOptionList对象为TRUE。


参数：...
Ignored
忽视


Details

详情----------Details----------

Currently, there are two main approaches for calculating the emission probabilities for diallelic genotypes.  Which approach is implemented depends on the value of ICE in the HmmOptionList object.
目前，有两种主要方法计算排放diallelic基因型概率。实施哪种方法取决于值ICEHmmOptionList对象。

When ICE is FALSE (the default), the emission probabilities for the diallelic genotypes are estimated from a Bernoulli(p_s) with p_s denoting the probability of a homozygous genotype ("AA" or "BB") for each state s. These probabilities can be specified in the constructor for the HmmOptionList class by the argument prGtHom. The corresponding probability for a heterozygous genotype ("AB") is 1-p_s for state s.
当ICE是FALSE（默认值），发射为diallelic基因型概率估计从伯努利（p_s）p_s表示纯合基因型（“AA”或“BB的概率每个国家的s ;)。这些概率可以指定参数HmmOptionListprGtHom类的构造。为杂合子基因型（“AB”）的相应的概率是1 p_s状态s。

For many calling algorithms, the genotypes are not called.  If many no-calls occur in a sample, this can indicate problems with the DNA quality.  No calls can also arise when there is poor separation of the genotype clusters or when the A and B allele intensities for a sample do not cluster into any of the diallelic genotype clusters.  No calls should be indicated by the value NA. We estimate the emission probability of a no-call using a Bernoulli(p2_s) with p2_s denoting the probability of a no call for state s. The numeric vector for p2 can be specified in the constructor for the HmmOptionList class through the argument prGtMis.
对于许多呼吁算法，不叫基因型。如果样品中发生的许多不调用，这可以表明与DNA的质量问题。没有检测也可以出现时有贫困基因型聚类分离或当样品A和B等位基因的强度不要到任何的diallelic基因型聚类的聚类。没有检测，应标明价值NA。我们估计没有调用p2_s表示没有呼叫的概率为国家s使用伯努利（p2_s）发射的概率。 p2数字矢量可以指定HmmOptionList类，通过在构造函数中的参数prGtMis。

When ICE is TRUE, we assume that the genotype calls were obtained from the crlmm.  This option is only available for a few of the platforms that crlmm supports.  The crlmm provides an estimate of the confidence for each diallelic genotype call.  For the HapMap dataset, we assessed the distribution of the confidence scores when the call was correct versus the distribution when the call was incorrect (using HapMap genotypes as the gold standard).  Using these distributions, we estimate the probability that the true diallelic genotype lies in a region of homozygosity (possibly suggesting a hemizygous deletion or a region of homozygosity induced by uniparental disomy) and the probability that the region has a 'normal' proportion of heterozygous genotypes. The constructor HmmOptionList has an argument rohStates that indicates which of the hidden states we expect homozygosity. See the reference below for additional details regarding the esimation of emission probabilities using the ICE option.
当ICE为TRUE，我们假定，从crlmm得到的基因型分型。此选项仅适用于少数crlmm支持的平台。 crlmm提供了一个信心的每个diallelic基因型分型的估计。 HapMap的数据集，我们评估的信心分数的分布，通话时与正确的分布是不正确的呼叫（使用HapMap的基因型作为金标准）。使用这些分布，我们估计，在纯合的区域（可能暗示半合子缺失或单亲二倍体诱导纯合的区域），该区域有一个正常杂合子基因型的比例和概率的的真实diallelic基因型的概率。构造HmmOptionListrohStates这显示隐藏状态，我们希望纯合的说法。见其他详细信息，参考下面有关esimation排放使用ICE选项的概率。


值----------Value----------

An array.  The dimensions are features x samples x states.
一个数组。尺寸x标本x状态功能。


注意----------Note----------

Only chromosomes 1-24 supported (23=X and 24 = Y).
支持1-24只染色体（23 = X和24 = y）。


作者（S）----------Author(s)----------



R.Scharpf




参考文献----------References----------

<h3>See Also</h3>   <code>cnEmission</code>, <code>gtEmission-methods</code>

举例----------Examples----------



data(oligoSetExample, package="oligoClasses")
oligoSet <- order(oligoSet)
oligoSet <- oligoSet[chromosome(oligoSet) == 1, ]
##[＃]
## Here, the probability of a missing genotype is 5 times as likely[＃在这里，缺少基因型的概率是5倍的可能性]
## for a homozygous-deletion than any of the other states[＃合子缺失比任何其他国家]
##[＃]
hmmOpts <- HmmOptionList(oligoSet, is.log=TRUE)

## Not run: [＃无法运行：]
## ICE is TRUE[＃冰是TRUE]
hmmOpts <- HmmOptionList(oligoSet, is.log=TRUE, ICE=TRUE)
tryCatch(gtEmission(oligoSet, hmmOpts), error=function(e) "Annotation platform not supported. See icePlatforms()")
annotation(oligoSet)

## for illustration[＃说明]
annotation(oligoSet) <- "genomewidesnp6"
gt.emit2 <- gtEmission(oligoSet, hmmOpts)
fit1 <- hmm(oligoSet, hmmOpts)
xyplot(cn ~ x | range, data=oligoSet, range=fit1, frame=2e6,
       panel=xypanel, cex=0.5, pch=21, border="orange",
       scales=list(x="free"))

## End(Not run)[＃结束（不运行）]


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