phastCons(rphast)
phastCons()所属R语言包：rphast
Produce conservation scores and identify conserved elements,...
保护成绩和确定保留下来的元素，...
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Produce conservation scores and identify conserved elements,
保护成绩和确定保留下来的元素，
用法----------Usage----------
transitions=NULL, estimate.rho=FALSE,
estimate.expected.length=FALSE, estimate.transitions=FALSE,
estimate.trees=FALSE, viterbi=TRUE, gc=NULL, nrates=NULL,
ref.idx=1, quiet=FALSE)
参数----------Arguments----------
参数：msa
An object of type msa representing the multiple alignment to be scored.
类型的对象，msa代表的多序列比对得分。
参数：mod
Either a single object of type tm, or a list containing two tm objects. If two objects are given, they represent the conserved and non-conserved phylogenetic models. If one is given, then this represents the non-conserved model, and the conserved model is obtained by scaling the branches by a parameter rho.
无论是单一类型的对象tm，或一个列表，其中包含两个tm对象。如果两个对象，它们代表了保守和非保守的亲缘模型。如果一个给定的，那么这代表的非保守的模型，和保守的模型是通过以下方式获得由一个参数rho沸石缩放分支。
参数：rho
Set the scale (overall evolutionary rate) of the model for the conserved state to be <rho> times that of the model for the non-conserved state ( 0 < rho < 1). If used with estimate.trees or estimate.rho, the specified value will be used for initialization only, and rho will be estimated. This argument is ignored if mod contains two tree model objects.
规模（整体进化速率）设置为的保守的状态是<rho>倍的模型，该模型的非保守的状态（0 <卢<1）。指定值如果使用与estimate.trees或estimate.rho，将用于初始化只，和rho将被估计。如果mod包含两个树模型对象，此参数将被忽略。
参数：target.coverage
A single numeric value, representing the fraction of sites in conserved elements. This argument sets a prior expectation rather than a posterior and assumes stationarity of the state-transition process. Adding this constraint causes the ratio of between-state transitions to be fixed at (1-gamma)/gamma (where gamma is the target.coverage value).
一个单一的数值，代表分数的网站中保留下来的元素。该参数设置之前的预期，而不是一个平稳的状态转换过程后，并假设。添加此约束会导致被固定在之间的状态转换的比率（1-γ）/γ（其中γ是target.coverage的值）。
参数：expected.length
A single numeric value, representing the parameter omega, which describes the expected length of conserved elements. This is an alternative to the transitions argument. If provided with target.coverage, than transition rates are fully determined, otherwise the target-coverage parameter will be estimated by maximum likelihood.
一个数值，表示该参数欧米茄，它描述了预期的保守元素的长度。这是一个替代的转换参数。 ，比如果与target.coverage提供转换率完全确定，否则目标覆盖参数将通过最大似然估计。
参数：transitions
(Alternative to target.coverage and expected.length; ignored if either of these are specified). A numeric vector of length one or two, representing the transition probabilities for the two-state HMM. The first value represents mu, the transition rate from the conserved to the non-conserved state, and the second value is nu, the rate from non-conserved to conserved. If only one value is provided then mu=nu. The rate of self-transitions are then 1-mu and 1-nu, and the expected lengths of conserved and non-conserved elements are 1/mu and 1/nu, respectively. If estimate.transition is TRUE, the provided values will be used for initialization.
（替代到target.coverage和expected.length;忽略，如果其中任一指定）。一个数值向量的长度为1或2，两状态HMM转移概率。第一个值表示亩，过渡率从保守的非保守的状态，和所述第二值是女，从非保守保守率。如果只提供一个值，然后亩= NU。的自转变的速率是1-mu和1-nu裸，预期长度保守和非保守的元素是1/mu 1/nu分别。如果estimate.transition是TRUE，提供的值，将用于初始化。
参数：estimate.rho
A logical value. If TRUE, Estimate the parameter rho (as described above), using maximum likelihood. Estimated value is reported in return list. This use is discouraged (see note below).
逻辑值。如果TRUE，估计参数卢（如上所述），用最大似然。报告估计值在返回的列表。不鼓励使用（见下文附注）。
参数：estimate.expected.length
A logical value. If TRUE, estimate the expected length of conserved elements by maximum likelihood, and use the target.coverage parameter for initialization. Setting this parameter to TRUE is discouraged (see note below).
逻辑值。如果TRUE，估计最大似然的预期长度的保守元素，并使用初始化参数target.coverage。设置此参数传递给TRUE不鼓励（看到下面的注释）。
参数：estimate.transitions
A logical value. If TRUE, estimate the transition rates between conserved and non-conserved states by maximum likelihood. The parameter transitions is then used for initialization. This argument is ignored if estimate.expected.length==TRUE. Setting this argument to TRUE is discouraged (see note below).
逻辑值。如果TRUE，估计保守和非保守状态之间的转换率最大似然法。的参数转换，然后用于初始化。此参数将被忽略如果estimate.expected.length == TRUE。将此参数设置为TRUE不鼓励（看到下面的注释）。
参数：estimate.trees
A logical value. If TRUE, estimate free parameters of tree models for conserved and non-conserved state. Setting this argument to TRUE is discouraged (see note below).
逻辑值。如果TRUE，估计树模型参数的保守和非保守的状态。将此参数设置为TRUE不鼓励（看到下面的注释）。
参数：gc
A single numeric value given the fraction of bases that are G or C, for optional use with estimate.trees or estimate.rho. This overrides the default behavior of estimating the base composition empirically from the data.
一个单一的数值给定的比例是G或C，可选与estimate.trees或estimate.rho使用的碱基。这将覆盖默认行为的经验从数据估计的基本组成。
参数：nrates
An integer vector of length one or two, for optional use with estimate.trees and a discrete-gamma model. Assume the specified number of rate categories, rather than the number given in the input tree model(s). If two values are given they apply to the conserved and nonconserved models, respectively.
整数向量的长度为1或2，随意使用，estimate.trees和一个独立的伽玛模式。假设指定数量的速率的类别，而不是在输入树模型（）给出的数字。如果两个值都给出了他们的保守和非保守的车型，分别适用于。
参数：viterbi
A logical value. If TRUE, produce discrete elements using the Viterbi algorithm.
逻辑值。如果TRUE，使用维特比算法的离散元件。
参数：ref.idx
An integer value. Use the coordinate frame of the given sequence. Default is 1, indicating the first sequence in the alignment. A value of 0 indicates the coordinate frame of the entire alignment.
一个整数值。使用的给定序列的坐标框架。默认值是1，表示第一个序列的对齐。值为0表示坐标系的整个路线。
参数：quiet
If TRUE, suppress printing of progress information.
如果TRUE，抑制打印进度信息。
Details
详细信息----------Details----------
A phylo-HMM consisting of two states is assumed: a "conserved" state and a "non-conserved" state. If two phylogenetic models are given, the first is the conserved state, and the second is the non-conserved state. If only one model is given, then this is used as the non-conserved state, and the conserved state is obtained by multiplying the branch lengths by the parameter
由两个国家组成的一个phylo-HMM假设：一个“保守”状态的“非保守”的状态。如果两个系统发育模型给出的，第一个是保守的状态，和所述第二非保守状态。如果只给出了一个模型，然后这是用来作为非保守的状态，和保守的状态是通过以下方式获得乘以分支长度由参数
值----------Value----------
A list containing parameter estimates. The list may have any of the following elements, depending on the arguments: <table summary="R valueblock"> <tr valign="top"><td>transition.rates</td> <td> A numeric vector of length two giving the rates from the conserved to the non-conserved state, and from the non-conserved to the conserved state.</td></tr> <tr valign="top"><td>rho</td> <td> The relative evolutionary rate of the conserved state compared to the non-conserved state.</td></tr> <tr valign="top"><td>tree.models</td> <td> Tree model objects describing the evolutionary process in the conserved and non-conserved states.</td></tr> <tr valign="top"><td>most.conserved</td> <td> An object of type feat which describes conserved elements detected by the Viterbi algorithm.</td></tr> <tr valign="top"><td>post.prob.wig</td> <td> A data frame giving a coordinate and score for individual bases in the alignment</td></tr> <tr valign="top"><td>likelihood</td> <td> The likelihood of the data under the estimated model.</td></tr></table>
一个列表，其中包含的参数估计。可能有以下元素的列表，根据参数的不同：<table summary="R valueblock"> <tr valign="top"> <TD> transition.rates</ TD> <td>一个数字矢量长度2给予速率从保守的非保守的状态，和从非保守的保守状态。</ TD> </ TR> <tr valign="top"> <TD>rho </ TD> <TD>进化速率相对保守的状态相比，非保守状态。</ TD> </ TR> <tr valign="top"> <TD>tree.models</ TD> <TD>树模型对象描述的进化过程中的保守和非保守的状态。</ TD> </ TR> <tr valign="top"> <TD> most.conserved </ TD> < TD>的对象的类型feat，它描述的维特比算法检测到的保守元素。</ TD> </ TR> <tr valign="top"> <TD>post.prob.wig </ TD> < TD> A的数据框对齐的各个碱基提供的坐标和得分</ TD> </ TR> <tr valign="top"> <TD> likelihood </ TD> <TD>的可能性根据估计模型的数据。</ TD> </ TR> </ TABLE>
注意----------Note----------
Estimating transition rates between states by maximum likelihood, or the parameters for the phylogenetic models, does not perform very well and is discouraged.
估计，或通过最大似然的系统发育模型的参数，状态的转换率之间没有很好地执行，被劝阻。
（作者）----------Author(s)----------
Melissa J. Hubisz and Adam Siepel
实例----------Examples----------
require("rphast")
exampleArchive <- system.file("extdata", "examples.zip", package="rphast")
files <- c("ENr334.fa", "rev.mod")
unzip(exampleArchive, files)
mod <- read.tm("rev.mod")
msa <- read.msa("ENr334.fa")
rv <- phastCons(msa, mod)
names(rv)
rv2 <- phastCons(msa, mod, estimate.trees=TRUE)
names(rv2)
rv2$tree.models
unlink(files)
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 2012-9-28 00:01:54
