wgaim-package(wgaim)
wgaim-package()所属R语言包：wgaim
Whole Genome Average Interval Mapping (wgaim) for QTL detection
全基因组的平均间隔的映射（wgaim）对QTL检测
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This package uses sophisticated mixed modelling methods with the addition of allowing a whole genome approach to detecting significant QTL in linkage maps.
此套件使用复杂的混合建模方法，增加了允许的全基因组检测到显着QTL在遗传连锁图谱的方法。
Details
详细信息----------Details----------
Package:
包装方式：
</td><td align="left"> wgaim
</ TD> <TD ALIGN="LEFT"> wgaim
Type:
类型：
</td><td align="left"> Package
</ TD> <TD ALIGN="LEFT">包装
Version:
版本：
</td><td align="left"> 1.1
</ TD> <TD ALIGN="LEFT"> 1.1
Date:
日期：
</td><td align="left"> 2011-10-24
</ TD> <TD ALIGN="LEFT"> 2011-10-24
License:
许可：
</td><td align="left"> GPL 2
</ TD> <TD ALIGN="LEFT"> GPL 2
Welcome to version 1.x of wgaim! The documentation given in this help file is only brief and users should eventually consult the soon to be released vignette that will be a companion to version 1.0 and above.
欢迎wgaim的1.x版本！本帮助文件中的文件是只有短暂的，最终用户应该咨询即将发布的小插曲，这将是一个伴侣1.0及以上版本。
Version 1.x package highlights:
版本1.x包亮点：
The inclusion of high dimensional genetic data
高维基因数据纳入
Users have a choice of whole genome marker or interval analysis.
用户有选择的全基因组标记或间隔分析。
Selection and estimation of QTL effects occurs using the implementation of Verbyla & Taylor (2011).
选择和估计的QTL效应发生，使用的实施Verbyla和泰勒（2011年）。
Deprecated functions:
已过时的功能：
read.interval: cross2int is the conversion function that should be used.
read.interval：cross2int是应该使用的转换函数，该函数。
wmerge: This function is not required as the genetic data is merged within the wgaim call.
wmerge：此功能不需要，作为的遗传数据合并在wgaim调用的。
This package builds on the qtl package of Broman by including additional functions for whole genome QTL analysis of a full linkage map using linear mixed models.
这个包的基础上qtl包Broman的附加功能包括一个完整的遗传图谱，利用线性混合模型的全基因组QTL分析。
The package provides a user friendly function cross2int for the conversion of "cross" objects created using read.cross in Bromans qtl package into an "interval" object or use in wgaim. Specifically, cross2int performs additional calculations for imputing missing values on each of the chromosomes across the full linkage map and also provides users with genetic distances and recombination fractions for the intervals. The returned object retains the class structure of an object created with read.cross and thus allows further use with the qtl package if desired.
该软件包提供了一个用户友好的功能cross2int转换的“cross”创建的对象使用read.cross在Bromans qtl封装成一个“interval的 “在wgaim的对象或使用。具体来说，cross2int执行额外的计算填充缺失值在整个连锁图谱的染色体上，还为用户提供的遗传距离和重组率的时间间隔。返回的对象保留与read.cross创建的对象的类结构，从而可以进一步使用qtl包，如果需要的话。
The package also provides a very neat graphical display of the chromosomes of a "cross" object. The method function link.map displays the full or subsetted linkage map according to chromosome or distance as well as displays non-overlapping marker names on the right hand side.
该软件包还提供了一个非常简洁的图形化显示的染色体的“cross”对象。的方法函数link.map显示染色体或距离以及根据显示的全部或子集的连锁图的右手侧上的非重叠的标记名称。
Modelling of the QTL's is achieved using the functions wgaim which, as its first argument, requires an asreml base model. Version 1.0 of wgaim allows users to include high dimensional genetic components in a wgaim analysis (See wgaim.asreml for more details or the soon to be released vignette companion to this version). For convenience the default tracing of results from the asreml models is outputted to a file for further inspection. For diagnostic purposes, the outlier statistics from each iteration can be viewed using out.stat. Diagnostics of the likelihood ratio test performed for each forward step can be displayed using tr.wgaim. The function also displays an incremental probability value matrix of the QTL ascertained at each forward step of the algorithm.
QTL的模拟实现使用功能wgaim，作为第一个参数，需要一个asreml示范碱基。 1.0版本的wgaim允许用户包括高维的遗传成分在wgaim分析（见wgaim.asreml了解更多详情或即将发布的这个版本的小插曲同伴）。为方便起见，默认跟踪结果从asreml车型的输出到一个文件中进行进一步的检查。用于诊断目的，每一次迭代的离群值统计，可以查看使用out.stat。每向前一步进行的似然比检验诊断可以显示使用tr.wgaim。该函数也显示的QTL的确定步骤，该算法在每个正向增量概率值矩阵。
Summary and print methods are available for the returned "wgaim" object and provide users with a detailed report on the QTL, their size, their flanking markers and significance (including LOD score). The returned "wgaim" object may also be plotted using the method function link.map. This function plots the full linkage map subsetted for chromosome and distance as well as provides shaded QTL regions and highlighted flanking markers. Plotting of QTL for multiple traits is also possible (see link.map.default)
摘要和print方法返回的“wgaim”对象，并为用户提供一份详细的报告上的QTL，它们的大小，标记和意义（包括LOD值）。返回的“wgaim”对象也可以使用的方法函数link.map绘制。此功能绘制完整的遗传连锁图谱以及子集染色体和距离的阴影的QTL区域和突出标记。绘制多个性状的QTL也可能（见link.map.default）
（作者）----------Author(s)----------
Julian Taylor, Simon Diffey, Ari Verbyla and Brian Cullis
Maintainer: Julian Taylor <julian.taylor@csiro.au>
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----------
qtl-package
qtl-package
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。
|
发表于 2012-10-1 21:04:59
