waffect-package(waffect)
waffect-package()所属R语言包：waffect
A package to simulate constrained phenotypes under a disease model H1
一个包来模拟约束下的一种疾病模型H1基因表型
译者：生物统计家园网 机器人LoveR
描述----------Description----------
waffect (pronounced 'double-u affect' for 'weighted affectation') is a package to simulate phenotypic (case or control) datasets under a disease model H1 such that the total number of cases is constant across all the simulations (the constrain in the title). The package also makes it possible to generate phenotypes in the case of more than two classes, so that the number of phenotypes belonging to each class is constant across all the simulations. waffect is used to assess empirically the statistical power of Genome Wide Association studies without generating genotypes for each simulation. The vignette includes a tutorial for performing such power studies.
waffect（发音为“双U影响”为“加权做作”）是一个包来模拟一种疾病模型H1的总数量是恒定的情况下，在所有的模拟表型（案例或控制）的数据集（限制在标题）。该程序包也使得人们有可能产生的表型中的两个以上的类的情况下，使属于每个类的表型的数目是恒定的，在所有的模拟。 waffect是用来评估经验的全基因组关联研究的统计力量，而不会产生基因型为每个模拟。小插曲，包括执行这种权力研究的教程。
Details
详细信息----------Details----------
waffect implements three alternative methods to simulate phenotypes with a fixed number of cases and controls and under a given disease model: i) an exact and efficient backward sampling algorithm; ii) a numerical Markov Chain Monte-Carlo (MCMC) approach; iii) a simple rejection algorithm. The backward algorithm is the default method. The rejection algorithm is deprecated. More details can be found in the companion article [1].
waffect实现了三个替代的方法来模拟固定数量的病例组和对照组，并根据给定的疾病模型：我的表型）的精确和有效的落后采样算法; II）的数值马尔可夫链蒙特卡罗方法（MCMC） ; iii）一个简单的抑制算法。落后的算法是默认的方法。抑制算法已经过时了。更多的细节可以发现，在本文的姊妹篇[1]。
安装和使用----------Installing and Using----------
To install this package, make sure you are connected to the Internet and issue the following command in the R prompt: install.packages("waffect")
安装该软件包，请确保您连接到互联网，并发出以下命令在R提示：install.packages("waffect")
To load the package in R: library(waffect)
装入包中R：library(waffect)
To open the .pdf file of the vignette: vignette("waffect-tutorial")
要打开pdf文件的小插曲：vignette("waffect-tutorial")
引用----------Citation----------
If you use waffect in published research, please cite the companion article:
如果你用waffect发表的研究报告中，引用本文的姊妹篇：
Perduca V, Sinoquet C, Mourad R, Nuel G: Alternative Methods for H1 Simulations in Genome-Wide Association Studies. Hum Hered 2012;73:95-104.
Sinoquet Perduca V，R，C，穆拉德作者Nuelĝ：H1模拟在全基因组关联研究的替代方法。的坎Hered 2012年73:95-104。
Type citation("waffect") for a BibTeX entry.
类型citation("waffect")的BibTEX项。
The authors would be glad to hear how waffect is employed. You are kindly encouraged to notify Gregory Nuel gregory.nuel@parisdescartes.fr and Vittorio Perduca vittorio.perduca@parisdescartes.fr about any work you publish that makes use of waffect.
作者是高兴听到如何waffect采用。您敬请通知格雷戈里作者Nuel gregory.nuel parisdescartes.fr和维托里奥Perduca的vittorio.perduca @ parisdescartes.fr任何的工作，你发布使用waffect的。
功能----------Functions----------
waffect high level function for simulating phenotypes in the binary (case/control) and mulitclass cases
waffect高级功能模拟二进制文件中的表型（件/控制）和mulitclass情况下
waffectbin low level function for simulating phenotypes in the binary case (not documented)
waffectbin低级别的功能，在二进制情况下的模拟表型（不记录）
数据集----------Datasets----------
This package comes with two datasets to be used for the fictive GWAs power analysis outlined in the vignette:
此包中附带了两个数据集，用于虚构的GWAS功率分析中列出的小插曲：
ped genotypic dataset in .ped format
ped基因型在.ped格式的数据集
map file in .map format describing the SNPs in the ped file
map文件.map格式描述的单核苷酸多态性在ped文件
The signals of association to be used in the fictive GWAs power analysis are also included:
中要使用的假想的GWAS功率分析相关联的信号，还包括：
p1_H0 Signal of association of the statistic S1 under H0
p1_H0协会的统计S1 H0信号
p1_H1 Signal of association of the statistic S1 under H1
p1_H1协会的统计H1 S1下的信号
p2_H0 Signal of association of the statistic S2 under H0
p2_H0信号的协会的统计S2下H0
p2_H1 Signal of association of the statistic S2 under H1
p2_H1信号的协会的统计S2下H1
参考文献----------References----------
参见----------See Also----------
Documentation for the function waffect. Useful information can be also found in the vignette: vignette("waffect-tutorial").
文件的功能waffect。有用的信息也可以被发现的小插曲：vignette("waffect-tutorial")。
实例----------Examples----------
## Not run: Typical usage to simulate case/control phenotypes under H1 (in this example: 5 individuals, 2 cases, 3 controls, the probability that individual 1 is a case is 0.5...):[＃不运行：模拟病例/对照表型在H1（在这个例子中：5个人，其中2例，3个控制个人的情况下为0.5的概率）的典型用法：]
waffect(prob = c(0.5, 0.2, 0.9, 0.7, 0.1), count = c(2,3), label = c(1,0))
## Not run: We can just specify the number of cases:[＃不运行的情况下，我们可以只指定数：]
waffect(prob = c(0.5, 0.2, 0.9, 0.7, 0.1), count = 2, label = c(1,0))
## Not run: We can change the labels:[＃不运行：我们可以改变标签：]
waffect(prob = c(0.5, 0.2, 0.9, 0.7, 0.1), count = 2, label = c("case", "control"))
## Not run: We can also simulate under H0 just entering the number of cases and controls:[＃不运行：刚刚进入一些病例组和对照组，我们还可以模拟在H0：]
waffect(count=c(2,3), label = c(1,0))
## Not run: Simulation of phenotypes in the multiclass case (in this example: 4 individuals and 3 classes, 1 individual in class 1, 2 individuals in class 2, 1 individual in class 3):[＃不运行：模拟在多类情况下的表型（在这个例子中：4个人，3个等级，1级1个人，2个人在2级，3级的1人）：]
pi = cbind(c(0.5,0.3,0.2), c(0.2,0.2,0.6), c(0.1,0.7,0.2), c(0.4,0.3,0.3))
waffect(prob = pi, count = c(1,2,1), label = 1:3)
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 2012-10-1 16:46:08
