colGxE(trio)
colGxE()所属R语言包：trio
Genotypic TDT for Gene-Environment Interactions
基因与环境相互作用的基因型TDT
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Performs a genotypic TDT for gene-environment interactions for each SNP represented by a column of a matrix in genotype format and a binary environmental factor. If alpha1 is set to a value smaller than 1, then the two-step procedure of Gauderman et al. (2010) will be used to first select all SNPs showing a p-value smaller than alpha1 in a logistic regression of the environmental factor against the sums of the codings for the parents' genotypes at the respective SNP. In the second step, the genotypic TDT is then applied to the selected SNPs.
执行基因型TDT基因与环境的相互作用为每个SNP的基因型格式和二进制环境因素的矩阵的列表示。如果alpha1被设置为一个值小于1时，则的Gauderman等两个步骤。 （2010）将用于第一选择所有SNP p值小于alpha1在Logistic回归分析环境因素对款项的父母在各自的SNP的基因型的编码。在第二步骤中，基因型的TDT，然后应用到所选择的单核苷酸多态性。
While colGxE computes the p-values based on asymptotic ChiSquare-distributions, colGxEPerms can be used to determine permutation-based p-values. Currently, no two-step procedure is provided for colGxEPerms.
虽然colGxE计算p-值渐近卡方分布的基础上，colGxEPerms可以用于确定置换基的p-值。目前，没有任何两个步骤的程序被设置为colGxEPerms。
用法----------Usage----------
colGxE(mat.snp, env, model = c("additive", "dominant", "recessive"),
alpha1 = 1, size = 50, addGandE = TRUE, whichLRT = c("both", "2df", "1df", "none"),
add2df = TRUE, addCov = FALSE, famid=NULL)
colGxEPerms(mat.snp, env, model = c("additive", "dominant", "recessive"),
B = 10000, size = 20, addPerms = TRUE, famid = NULL, rand = NA)
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：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：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：alpha1
a numeric value between 0 and 1 (excluding 0). If alpha1 = 1, all SNPs will be tested with a genotypic TDT. Otherwise, the two-step procedure of Gauderman et al. (2010) will be used to select all SNPs showing a p-value smaller than or equal to alpha1 in a logistic regression in which the environmental factor is used as response and the sums over the codings for the genotypes of the parents are employed as predictor. The genotypic TDT will then be applied to the selected SNPs. Since a logistic regression is employed in the first step, which requires a numerical determination of the parameter estimates, the two-step procedure will not lead to a reduction in computing time, but will increase the computing time.
一个数字的值在0和1之间（但不包括0）。如果alpha1 = 1，所有SNP位点进行测试与基因型TDT。否则，两个步骤的Gauderman等。 （2010），将用于选择所有SNP示出了p-值小于或等于到alpha1在其中的环境因素是用来作为响应的款项的父母的基因型的编码中的Logistic回归作为预测指标。然后将被施加到所选择的单核苷酸多态性的基因型的TDT。由于是Logistic回归采用在第一步骤中，这需要的参数估计值的数值判定，两个步骤将不会导致在计算时间减少，但会增加计算时间。
参数：size
the number of SNPs considered simultaneously when computing the parameter estimates.
数个SNP位点同时考虑时，计算参数估计值。
参数：addGandE
should the ORs and their confidence intervals for the exposed cases be added to the output?
OR和暴露的情况下，其置信区间为被添加到输出？
参数：whichLRT
character string specifying which likelihood ratio test should be added to the output. If "2df", 2 degree of freedom likelihood ratio tests comparing the fitted models (containing one parameter for the SNP and one for the gene-environment interaction) with models containing no factor will be performed. If "1df", one degree of freedom likelihood ratio tests comparing the fitted model (containing two parameters, one for the SNP and the other for the interaction) with models only containing the respective SNP will be added to the output. If "both" (default), both tests will be performed, whereas none test will be done, if whichLRT = "none".
似然比检验应该被添加到输出的字符串特别指定。如果"2df"，将进行2度比较自由似然比检验的任何因素模型的拟合模型（含一个参数的SNP和基因与环境之间的相互作用）。如果"1df"，1度的自由似然比测试，比较拟合模型（含有两个参数，一个为SNP和其他的相互作用）与仅包含各自的SNP的模型将被添加到输出。如果"both"（默认值），这两个测试将被执行，而没有测试将完成，如果whichLRT = "none"。
参数：add2df
should the results of a 2 df Wald test for testing both the SNP and the interaction effect simultaneously be added to the model?
2 DF Wald检验测试的SNP的互动效应的结果，同时应该被添加到模型中？
参数：addCov
should the covariance between the parameter estimations for the SNP and the gene-environment interaction be added to the output? Default is addCov = FALSE, as this covariance is given by the negative variance of the parameter estimate for the SNP.
应该被添加到输出之间的协方差参数估计的单核苷酸多态性以及基因与环境之间的相互作用？默认是addCov = FALSE，协方差的负面方差参数估计的SNP。
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：B
number of permutations.
的排列数。
参数：addPerms
should the matrices containing the permuted values of the test statistics for the SNP and the gene-environment interaction be added to the output?
应的矩阵包含置换为SNP和基因与环境的相互作用的检验统计量的值被添加到输出？
参数：rand
integer for setting the random number generator into a reproducible state.
整数随机数发生器设置成再生状态。
Details
详细信息----------Details----------
A conditional logistic regression model including two parameters, one for G, and the other for GxE, is fitted, where G is specified according to model.
一个条件Logistic回归模型包括两个参数，一个为G，和其他GxE，安装，，其中G指定根据model。
值----------Value----------
For colGxE, an object of class colGxE consisting of the following numeric matrices with two columns (one for each parameter):
对于colGxE，类的一个对象colGxE组成的两列（对于每个参数之一）以下的数值矩阵：
参数：coef
the estimated parameter,
估计参数，
参数：se
the estimated standard deviation of the parameter estimate,
估计标准差的参数估计，
参数：stat
Wald statistic,
Wald统计量，
参数：OR
the odds ratio, i.e.\ exp(coef) </table>
的比值比，即\exp(coef)</ TABLE>
,
，
参数：lowerOR
the lower bound of the 95% confidence interval for OR,
下限的95％置信区间OR，
参数：upperOR
the upper bound of the 95% confidence interval for OR,
上限的95％置信区间OR，
参数：usedTrios
the number of trios affecting the parameter estimation,
影响参数估计的三重奏，
参数：env
vector containing the values of the environmental factor,
向量的环境因素的值，
参数：type
model,
model，
参数：addGandE
the value of addGandE,
的价值的addGandE，
参数：addOther
a logical vector specifying which of the likelihood ratio tests and if the 2 df Wald test was performed,
指定逻辑向量的似然比测试，如果进行2 df的Wald检验，
and depending on the specifications in colGxE
根据不同的规格在colGxE
参数：cov
numeric vector containing the covariances,
数字向量的协方差，
参数：lrt2df
a numeric matrix with two columns, in which the first column contains the values of the 1 df likelihood ratio test statistic and the second the corresponding p-values,
数值具有两列的矩阵，其中，第一列包含的自由度为1的似然比检验统计量的值和第二相应的p-值，
参数：wald2df
a numeric matrix with two columns, in which the first column contains the values of the 2 df Wald test statistics and the second the corresponding p-values,
数值具有两列的矩阵，其中，第一列包含的值的2自由度Wald检验统计和第二相应的p-值，
参数：lrt1df
a numeric matrix with two columns, in which the first column contains the values of the 2 df likelihood ratio test statistic and the seocnd the corresponding p-values.
具有两列的矩阵，其中，第一列包含2 df的似然比检验统计量和seocnd相应的p-值的值的一个数字。
For colGxEPerms,
对于colGxEPerms，
参数：stat
a matrix with two columns containing the values of gTDT statistics for the main effects of the SNPs and the gene-environment interactions when considering the original, unpermuted case-pseudo-control status,
包含值的gTDT统计的单核苷酸多态性以及基因与环境相互作用的主要影响考虑原，unpermuted的情况下，伪控制状态时，有两列矩阵，
参数：pval
a matrix with two columns comprising the permutation-based p-values corresponding to the test statistics in stat,
含有的置换基于p-值在stat的检验统计量对应于具有两列的矩阵，
and if addPerms = TRUE
如果addPerms = TRUE
参数：matPermG
a matrix with B columns containing the values of the gTDT statistic for the SNPs when considering the B permutations of the case-pseudo-control status,
矩阵B列的值的gTDT统计，单核苷酸多态性考虑B排列的情况下，伪控制状态时，
参数：matPermGxE
a matrix with B columns containing the values of the gTDT statistic for the gene-environment interactions when considering the B permutations of the case-pseudo-control status.
一个矩阵与B列中包含的值时，基因与环境相互作用的gTDT统计考虑B的排列的情况下，伪控制状态。
（作者）----------Author(s)----------
Holger Schwender, <a href="mailto:holger.schwender@udo.edu">holger.schwender@udo.edu</a>
参考文献----------References----------
Efficient Genome-Wide Association Testing of Gene-Environment Interaction in Case-Parent Trios. American Journal of Epidemiology, 172, 116-122.
Rapid Testing of SNPs and Gene-Environment Interactions in Case-Parent Trio Data Based on Exact Analytic Parameter Estimation. Biometrics. DOI: 10.1111/j.1541-0420.2011.01713.x.
参见----------See Also----------
colTDT, ped2geno
colTDT，ped2geno
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 12:04:59
