wgaim.asreml(wgaim)
wgaim.asreml()所属R语言包：wgaim
wgaim method for class "asreml"
wgaim方法类“asreml”
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Fits an iterative Whole Genome Average Interval Mapping (wgaim) model for QTL detection
适用于一个迭代的QTL检测全基因组平均区间作图（wgaim）模型
用法----------Usage----------
## S3 method for class 'asreml'
wgaim(baseModel, phenoData, intervalObj, merge.by = NULL,
gen.type = "interval", method = "random", TypeI = 0.05, attempts = 5,
trace = TRUE, verboseLev = 0, ...)
参数----------Arguments----------
参数：baseModel
a model object of class "asreml" usually representing a base model with which to build the qtl model.
一个模型类的对象“asreml”通常代表一个基本模型建立的QTL模型。
参数：phenoData
a data frame containing the phenotypic elements used to fit baseModel. This data is checked against the base models data
一个数据框包含的表型元素，以适应baseModel。检查这些数据对基本模型数据
参数：intervalObj
a list object containing the genotypic data, usually an "interval" object obtained from using cross2int. This object may contain many more markers than observations (see Details).
一个列表对象，其中包含的基因型数据，通常是“interval”对象使用cross2int。这个对象可能包含更多的观测指标（见详情）。
参数：merge.by
a character string or name of the column(s) in phenoData and intervalObj to merge the phenotypic and genotypic data sets.
一个字符串或名称的列（S）phenoData和intervalObj合并的表型和基因型数据集。
参数：gen.type
a character string determining the type of genetic data to be used in the analysis. Possibilities are "interval" and "markers". The default is "interval". (see Details).
一个字符串确定遗传在分析中要使用的数据的类型。可能是“interval”，“markers”。默认值是“interval”。 （见详情）。
参数：method
a character string determining the type of algortithm to be used in the analysis. Possibilities are "random" and "fixed". The default is "random". (see Details).
确定要在分析中使用的类型的algortithm一个字符串。可能是“random”，“fixed”。默认值是“random”。 （见详情）。
参数：TypeI
a numerical value determining the level of significance for detecting a QTL. The default is 0.05.
确定显着性水平的数值，用于检测的QTL。默认值是0.05。
参数：attempts
An integer representing the number of attempts at convergence for the fixed or random qtl model. The default is 5.
一个整数，表示数固定或随机的QTL模型收敛的尝试。默认值是5。
参数：trace
An automatic tracing facility. If trace = TRUE then all asreml output is piped to the screen during the analysis. If trace = "file.txt", then output from all asreml models is piped to "file.txt". Both trace machanisms will display a message if a QTL is detected.
自动跟踪功能。如果trace = TRUE然后所有的asreml输出通过管道输送到屏幕上的分析过程中。如果trace = "file.txt"，然后通过管道输送到输出所有asreml车型“file.txt”。如果检测到的QTL，两种跟踪的machanisms将显示一条消息。
参数：verboseLev
numerical value, either 0 or 1, determining the level of tracing outputted during execution of the algorithm A 0 value will produce the standard model fitting output from the fitted ASReml models involved in the forward selection. A value of 1 will add a table of Chromosome and Interval outlier statistics for each iteration
数值，为0或1，确定的跟踪输出的算法执行过程中的0值将涉及在正向选择从拟合ASReml的模型产生的标准模型拟合输出的电平。值为1将添加一个表格的染色体和间隔离群统计，每一次迭代
参数：...
Any other extra arguments to be passed to each of the asreml calls. These may also include asreml.control arguments.
任何其他的额外的参数被传递到每个asreml调用。这些可能还包括asreml.control参数。
Details
详细信息----------Details----------
In the initial call to wgaim.asreml, the marker or interval information is collated from intervalObj. If gen.type = "interval" then midpoints of intervals are collated from the "intval" component of intervalObj. If gen.type = "markers" then markers are collated from the "imputed.data" component of intervalObj (It should be noted that a "marker" analysis is less efficient than an "interval" analysis as it does not take into account the correlation of the marker effects in the specificity of the model; see Verbyla et. al, 2007).
在初始调用wgaim.asreml，标记或间隔信息的整理intervalObj。如果gen.type = "interval"然后区间的中点整理“intval”组成部分intervalObj。如果gen.type = "markers"然后标记从“imputed.data”组件整理intervalObj（应当指出，一个“marker”分析是效率较低的比的“interval”分析，因为它不考虑到相关的标记物的特异性效应模型，见Verbyla等人，2007年）。
The method argument in wgaim.asreml allows the user access to two algorithms. If method = "fixed" then the forward selecction algorithm uses the legacy code packaged with pre-1.0 versions of wgaim. This code uses the chromosome statistics as a guide to its selection of QTL. This selection process is now known to be flawed when small linkage groups are present. For this reason it is suggested that this option only be used when there are a moderate number of markers on each linkage group.
method参数wgaim.asreml两种算法允许用户访问。如果method = "fixed"然后正向selecction算法使用的遗留代码打包带1.0之前的版本的wgaim。此代码使用的染色体作为指导其选择的QTL的统计数据。这个选择过程是有缺陷的，现在被称为小个连锁群存在。出于这个原因，建议此选项时，仅可用于有中等数量的每个连锁群上的标记。
This version of wgaim allows high dimensional marker information to be analysed. A simple transformation of the collated high dimensional marker set shows that it may be reduced to the number of genetic lines used in the analysis. This transformation is internal to the wgaim.asreml call and users can now expect a considerably large acceleration in the performance of wgaim.
此版本的wgaim允许高维标记信息进行分析。整理高维标记集的一个简单的变换显示，它在分析中使用的遗传线的数目可以减少。这种转变是内部的wgaim.asreml调用，用户现在可以预期一个相当大的加速度的性能wgaim。
It is recommended that trace = "file.txt" be used to pipe the sometimes invasive tracing of asreml licensing and fitting numerics for each model to a file. Errors, warnings and messages will still appear on screen during this process. Note some warnings that appear may be passed through from an asreml call and are outputted upon exit. These may be ignored as they are handled during the execution of the function.
建议trace = "file.txt"使用asreml发牌及配件数值显示每个模型的文件有时侵入性追踪管。错误，警告和消息仍然会出现在屏幕上，在这个过程中。注意出现一些警告可能会通过从asreml呼叫，并在退出时输出。这些可能被忽略，因为它们的功能的执行过程中处理。
值----------Value----------
An object of class "wgaim" which also inherits the class "asreml" by default. The object returned is actually an asreml object (see asreml.object) with the addition of components from the QTL detection listed below.
类的一个对象“wgaim”，这也继承类“asreml”默认的。返回的对象实际上是一个asreml对象（见asreml.object）与另外的组件从下面列出的QTL检测。
参数：QTL
A list of components from the significant QTL detected including a character vector of the significant QTL along with a vector of the QTL effect sizes. There are also a number of diagnostic meausres that can be found in diag that are used in conjunction with tr.wgaim and out.stat.
包括一个字符随着QTL效应大小的向量，向量的显着QTL的显着QTL检测的组件列表。也有一些诊断meausres，可以发现在diag，一起tr.wgaim和out.stat。
（作者）----------Author(s)----------
Julian Taylor, Simon Diffey, Ari Verbyla and Brian Cullis
参考文献----------References----------
average interval mapping and a random effects formulation. Theoretical and Applied Genetics. Submitted.
Bi-Parental Populations Using Linear Mixed Models. Journal of Statistical Software, 40(7), 1-18. URL http://www.jstatsoft.org/v40/i07/.
by simultaneous use of the full linkage map. Theoretical And Applied Genetics, 116, 95-111.
参见----------See Also----------
print.wgaim, summary.wgaim
print.wgaim，summary.wgaim
实例----------Examples----------
## Not run: [＃不运行：]
# read in data[读入数据]
data(zinc, package = "wgaim")
data(raccas, package = "wgaim")
# subset linkage map and convert to "interval" object[子集遗传连锁图谱，并将其转换为“间隔”对象]
raccas <- subset(raccas, chr = c("1A1", "2D1", "4D2", "6A1"))
raccas <- cross2int(raccas, missgeno = "Martinez")
# base model[示范碱基]
zn.fm <- asreml(znconc ~ Type, random = ~ Block + id, data = zinc)
# find QTL's[发现QTL的]
zn.qtl <- wgaim(zn.fm, phenoData = zinc, intervalObj = raccas,
merge.by = "id", trace = "trace.txt", na.method.X = "include")
## End(Not run)[＃（不执行）]
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 2012-10-1 21:05:06
