scoreTDT(trio)
scoreTDT()所属R语言包：trio
Score Tests for SNPs, GxE, and GxG Interactions
为SNP位点，GXE，GXG相互作用的分数测试
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Performs score tests for all individual SNPs (scoreTDT), all interactions of each SNP with an environmental variable (scoreGxE), or all interactions of two SNPs (scoreGxG) comprised by an input matrix based on the same log-likelihood considered in the corresponding genotypic TDT, where in scoreGxG the conditional logistic regression model including only one parameter (for the interaction effect) is used.
执行评分测试的所有个人单核苷酸多态性（scoreTDT），所有的环境变量（每个SNP位点的相互作用scoreGxE），或相互作用的两个单核苷酸多态性（scoreGxG）由输入矩阵基于相同的对数似然认为在相应的基因型TDT，在scoreGxG使用条件Logistic回归模型只有一个参数的互动效应。
Additionally, the maximum over the score statistics for testing an additive, dominant, and recessive effect can be determined using scoreMaxStat.
此外，在得分统计测试的添加剂最大，占主导地位，显性和隐性的影响可以使用scoreMaxStat，确定。
用法----------Usage----------
scoreTDT(mat.snp, model = c("additive", "dominant", "recessive"), size = 20)
scoreGxE(mat.snp, env, model = c("additive", "dominant", "recessive"), size = 20,
famid = NULL)
scoreGxG(mat.snp, model = c("additive", "dominant", "recessive"), genes = NULL,
size = 20)
scoreMaxStat(mat.snp, size = 20)
## S3 method for class 'scoreTDT'
print(x, top = 5, digits = 4, ...)
## S3 method for class 'scoreGxE'
print(x, top = 5, digits = 4, onlyGxE = FALSE, ...)
## S3 method for class 'maxScoreTrio'
print(x, top = 5, digits = 4, ...)
参数----------Arguments----------
参数：mat.snp
a numeric matrix in which each column represents a SNP. Each column must be a numeric vector of length 3 * t representing a SNP genotyped at t trios. Each of the t blocks must consist of the genotypes of father, mother, and offspring (in this order). The genotypes must be coded by 0, 1, and 2. Missing values are allowed and need to be coded by NA. This matrix might be generated from a ped-file by, e.g., employing ped2geno.
一个数字矩阵，其中每一列代表一个SNP。每列必须是一个数值向量的长度3 * t较SNP基因分型t三重奏。 t块必须由基因型的父亲，母亲和后代（按照这个顺序）。必须被编码的基因型，0，1，和2。遗漏值是允许的，需要进行编码NA。这个矩阵可能会产生的一个PED文件，例如，采用ped2geno。
参数：model
type of model that should be fitted. Abbreviations are allowed. Thus, e.g., model = "dom" will fit a dominant model, and model = "r" an recessive model.
应嵌合的模型，该模型的类型。缩写是允许的。因此，例如，model = "dom"会适合一个占主导地位的模式，和model = "r"隐性模型。
参数：size
the number of models considered simultaneously when computing the parameter estimates.
同时考虑模型的数量时，计算参数估计值。
参数：env
a vector of length t (see mat.snp) containing for each offspring the value of a binary environmental variable, which must take the values 0 and 1.
一个向量的长度t（见mat.snp）为每个后代含有一个二进制的环境变量的值，必须采取的值在0和1。
参数：famid
a vector of the same length as env specifying the family IDs for the corresponding values of the environmental variable in env. Can be used to reorder the vector env when the order of the trios differs between env and mat.snp.
相同的长度的矢量env指定的家庭环境变量的相应值的ID在env。可用于重新排序向量env的三重奏的顺序是不同的env和mat.snp。
参数：genes
a character vector containing the names of the genes (or LD-blocks or other genetic sets of SNPs) to which the SNPs belong. If specified, only the two-way interactions between SNPs from different genes (or LD-blocks or other genetic sets of SNPs) are tested. If NULL, all two-way interactions between all possible pairs of SNPs are tested.
字符向量的名称（或LD块或其他基因组的单核苷酸多态性）的基因的单核苷酸多态性属于。如果指定的话，只有从不同的基因的单核苷酸多态性之间的双向互动（或LD块或其他基因组的单核苷酸多态性）的测试。如果NULL，对所有可能的SNP位点之间的双向互动测试。
参数：x
an object of class scoreTDT, scoreGxE, or maxScoreTrio, i.e. the output of the function scoreTDT / scoreGxG, scoreGxE, or scoreMaxStat, respectively.
类的一个对象scoreTDT，scoreGxE或maxScoreTrio，即输出的功能scoreTDT/scoreGxG，scoreGxE或scoreMaxStat“。
参数：digits
number of digits that should be printed.
应打印的数字。
参数：top
number of interactions that should be printed. If the number of interactions is smaller than or equal to top, then the statistics for all interactions are printed in the order of their computation. Otherwise, the top interactions with the smallest p-values are printed.
应该打印的交互数。如果交互的数目小于或等于top，然后可用于所有相互作用的统计信息被印在它们的计算的顺序。否则，top与最小的p-值的相互作用被打印出来。
参数：onlyGxE
logical indicating whether only the statistics for the parameter of the GxE interaction should be printed. If FALSE, the statistics for both parameters in the model are shown.
逻辑指示是否只应打印的统计参数的GXE相互作用。如果FALSE，这两个参数在模型中显示的统计数据。
参数：...
ignored.
忽略不计。
值----------Value----------
For scoreTDT and scoreGxG, an object of class scoreTDT containing numeric vectors
对于scoreTDT和scoreGxG，对象的类scoreTDT包含数字向量
参数：score
the scores for all SNPs or SNP interactions,
所有SNP，SNP相互作用的分数，
参数：info
the denominators of the corresponding score statistics </table>
相应的分数统计的分母</ TABLE>
,
，
参数：stat
the values of the score statistics for all SNPs or SNP interactions </table>
值的得分统计的所有SNP位点或SNP相互作用</ TABLE>
,
，
参数：pval
the corresponding p-values computed based on a ChiSquare-distribution with 1 degree of freedom.
计算相应的p-值与自由度为1的基础上的，卡方分布。
（作者）----------Author(s)----------
Holger Schwender, <a href="mailto:holger.schwender@udo.edu">holger.schwender@udo.edu</a>
参见----------See Also----------
colTDT, colGxE, colTDT2way
colTDT，colGxE，colTDT2way
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 12:06:56
