HmmOptionList(VanillaICE)
HmmOptionList()所属R语言包：VanillaICE
Constructors for HmmOptionList class
为HmmOptionList类的构造
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Constructors for HmmOptionList class. An object of the class contains most of the options for fitting the HMM.
为HmmOptionList类的构造。一个类的对象包含了装修的HMM的大部分股权。
用法----------Usage----------
HmmOptionList(object, copynumberStates,
states, ICE = FALSE, is.log = FALSE,
scaleSds = TRUE,
log.initialPr = log(rep(1/length(states), length(states))),
normalIndex, prGtHom,
prGtMis = rep(1/length(states), length(states)),
prHetCalledHom = 0.001, prHetCalledHet = 0.995,
prHomInNormal = 0.8, prHomInRoh = 0.999,
rohStates, tau = 1e+08, a2n = 1, n2a = 1, a2a = 1,
verbose = 2L, ...)
hmm.setup(object, ...)
参数----------Arguments----------
参数：object
Object of class SnpSet or one of its derivatives.
对象的类SnpSet或它的衍生物之一。
参数：copynumberStates
numeric. The mean values for each of the hidden states. Ignored if object is not a CopyNumberSet, oligoSnpSet, or CNSet.
数字。每个隐藏状态的平均值。忽略object如果是不是CopyNumberSet，oligoSnpSet或CNSet。
参数：states
Character vector indicating the names of the hidden states
特征向量表示的隐藏状态的名称
参数：ICE
Logical. Whether to use crlmm confidence scores estimates for computing the emission probabilities of the genotype calls. Only supported for some platforms. See details.
逻辑。是否使用crlmm信心分数的计算基因型分型的发射概率估计。仅支持一些平台。查看详情。
参数：is.log
Logical. Whether the copy number estimates in object are on the log scale. See details
逻辑。无论拷贝数估计在object的log上规模。查看详情
参数：scaleSds
Not implemented. [[Factor to scale the standard deviations used to compute the emission probabilities.]]
没有落实。 [[扩展，用来计算发射概率的标准偏差的因素。]]
参数：log.initialPr
Numeric vector of the same length as the number of states. Specifies the initial state probabilities on the log scale.
数字的国家数目相同长度的向量。指定log规模的初始状态的概率。
参数：normalIndex
Integer. Indicates which element of the states vector corresponds to the 'normal' state.
整数。表明该元素的states向量对应的“正常”状态。
参数：prGtHom
numeric vector in [0,1], Elements correspond to the probability of a homozygous genotype for each state. Ignored for CopyNumberSet objects.
数字向量，在[0,1]元素对应为每个国家的纯合基因型的概率。忽略CopyNumberSet的对象。
参数：prGtMis
numeric vector in [0,1], Elements correspond to the probability of a missing genotype for each state. Ignored for CopyNumberSet objects.
数字向量，在[0,1]元素对应为每个国家的失踪基因型的概率。忽略CopyNumberSet的对象。
参数：prHetCalledHom
numeric in [0,1]. The probability of a heterozygous genotype incorrectly called homozygous. Ignored if object is a CopyNumberSet objects or if ICE is FALSE.
在[0,1]数字。杂合基因型的概率被错误地称为纯合子。被忽略，如果对象是一个CopyNumberSet对象或如果冰是FALSE。
参数：prHetCalledHet
numeric in [0,1], The probability of a heterozygous genotype correctly called heterozygous. Ignored if object is a CopyNumberSet or if ICE is FALSE.
在[0,1]数字，正确地称为杂合子的杂合基因型的概率。被忽略，如果对象是一个CopyNumberSet或者如果ICE是FALSE。
参数：prHomInNormal
numeric in [0,1]. The probability of a homozygous genotype in a region with copy number two. Ignored if ICE is FALSE or if object is a CopyNumberSet.
在[0,1]数字。在一个区域拷贝数二的纯合基因型的概率。被忽略，如果ICE是假的，或者如果对象是一个CopyNumberSet。
参数：prHomInRoh
numeric in [0,1]. The probability of observing a homozygous genotype when only homozygous genotypes are expected (e.g., hemizygous deletions, copy-neutral regions of homozygosity). Ignored if ICE is FALSE or if object is a CopyNumberSet.
在[0,1]数字。预计只有纯合子基因型的时候（例如，半合缺失，纯合子副本中立区域）的观察合子基因型的概率。被忽略，如果ICE是假的，或者如果对象是一个CopyNumberSet。
参数：rohStates
integer vector. Indicates which states only homozygous genotypes are expected. Ignored if ICE is FALSE or if object is a CopyNumberSet.
整数向量。指示指出预计只有纯合子基因型。被忽略，如果ICE是假的，或者如果对象是一个CopyNumberSet。
参数：tau
Numeric. Factor for scaling the distance weighted transition probability. See details.
数字。缩放距离加权跃迁几率的因素。查看详情。
参数：a2n
Integer. Factor for scaling the probability of transitioning from an altered state to a normal state. Default is 1 (recommended).
整数。为扩大从改变状态过渡到正常状态的概率的因素。默认值是1（推荐）。
参数：n2a
Integer. Factor for scaling the probability of transitioning from the normal state to an altered state. Default is 1 (recommended).
整数。过渡到正常状态改变状态的概率为扩大因素。默认值是1（推荐）。
参数：a2a
Integer. Factor for scaling the probability of transitioning from an altered state to a different altered stateDefault is 1 (recommended).
整数。过渡到不同改变stateDefault的改变状态的概率为扩大的因素是：1（推荐）。
参数：verbose
Logical. Whether to display all messages and warnings.
逻辑。是否显示所有的消息和警告。
参数：...
For hmm.setup, additional arguments passed to HmmOptionList constructor. Ignored for HmmOptionList.
“hmm.setup，额外的参数传递给HmmOptionList构造。 HmmOptionList忽略。
Details
详情----------Details----------
Setting ICE to TRUE requires availability of the crlmm confidence scores for HapMap samples. Currently only a few platforms are supported. See VanillaICE:::icePlatforms().
设置ICE真需要HapMap的样品crlmm信心分数的可用性。目前只有少数几个平台都支持。看到VanillaICE:::icePlatforms()。
The transition probability is computed as exp(-2 * d/tau), where d is the distance between two loci. The default value for tau 10^(8), but users can adjust this number to control the smoothness of the resulting HMM.
转移概率计算exp(-2 * d/tau)，其中d是两个位点之间的距离。默认值tau10^(8)，但用户可以调整这个数字，以控制所产生的HMM平滑。
For object classes that do not support copy number estimation (e.g., SnpSet), is.log is ignored. For all other classes, is.log is used to determine the plausible range of copy number estimates. When is.log is TRUE, we assume the range of the copy number estimates is [-10, 2.5]. Otherwise, the range of the copy number estimates is assumed to be [0, 10]. Values more extreme are truncated. The emission probabilities from the HMM are estimated by fitting a Gaussian-Uniform mixture. The uniform component of the mixture model has a support indicated by the above ranges. The Gaussian component has a mean for each state that is provided by the copynumberStates argument. For oligoSnpSet objects, the standard deviation of the Gaussian can be marker- and sample-specific if confidence scores are provided in the cnConfidence assay data element of the oligoSnpSet object. Specifically, 1/cnConfidence is used as the standard deviation. If the cnConfidence slot is not specified, the median absolute deviation of the copy number estimates across autosomal chromosomes is used for the standard deviation of both autosomal and sex chromosome markers.
object类不支持拷贝数估计（例如，SnpSet）is.log被忽略。对于所有其他类，is.log拷贝数的估计，以确定合理的范围。当is.log是真的，我们承担的拷贝数估计的范围是[-10，2.5]。否则，拷贝数的估计范围内被认为是[0，10]。更极端的值将被截断。拟合高斯均匀混合的HMM发射概率估计。均匀混合模型组件具有上述范围表示支持。高斯组件有一个copynumberStates参数，平均每个国家提供。 oligoSnpSet对象，标准差的高斯可以是特定标记和样品，如果信心指数在cnConfidence检测数据元素oligoSnpSet对象提供。具体来说，1/cnConfidence作为标准偏差。如果没有指定cnConfidence插槽，跨越常染色体的拷贝数估计的中位数绝对偏差用于对常染色体和性染色体标记的标准偏差。
值----------Value----------
Object of class HmmOptionList.
对象类HmmOptionList。
作者（S）----------Author(s)----------
Rob Scharpf
参见----------See Also----------
HmmOptionList, oligoSnpSet, SnpSet, SnpSet, CopyNumberSet
HmmOptionList，oligoSnpSet，SnpSet，SnpSet，CopyNumberSet
举例----------Examples----------
if(require("crlmm")){
data(cnSetExample, package="crlmm")
hmm.params <- HmmOptionList(cnSetExample)
hmm.params
}
data(oligoSetExample, package="oligoClasses")
hmm.params <- HmmOptionList(oligoSet)
hmm.params
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。
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发表于 2012-2-26 15:55:33
