single.snp.tests(chopsticks)
single.snp.tests()所属R语言包：chopsticks
1-df and 2-df tests for genetic associations with SNPs
单核苷酸多态性的遗传协会1-DF和2-DF测试
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function carries out tests for association between phenotype and a series of single nucleotide polymorphisms (SNPs), within strata defined by a possibly confounding factor. SNPs are considered one at a time and both 1-df and 2-df tests are calculated. For a binary phenotype, the 1-df test is the Cochran-Armitage test (or, when stratified, the Mantel-extension test).
协会之间的表型和系列的单核苷酸多态性（SNP）在可能的混杂因素定义的阶层，此功能进行了测试。 SNPs被认为在一次和两个1-DF和2-DF测试计算。对于一个二进制型，1-DF测试是科克伦 - 阿米蒂奇测试（或，当分层，的曼特尔扩展测试）。
用法----------Usage----------
single.snp.tests(phenotype, stratum, data = sys.parent(), snp.data, subset, snp.subset)
参数----------Arguments----------
参数：phenotype
A vector containing the values of the phenotype
一个向量，包含的表型值
参数：stratum
Optionally, a factor defining strata for the analysis
或者，定义一个因素的分析阶层
参数：data
A dataframe containing the phenotype and stratum data. The row names of this are linked with the row names of the snps argument to establish correspondence of phenotype and genotype data. If this argument is not supplied, phenotype and stratum are evaluated in the calling environment and should be in the same order as rows of snps
一个dataframephenotype和stratum数据。此行的名称与该行建立的表型和基因型数据通信snps参数名。如果这种说法是不提供的，phenotype和stratum在调用环境评估，并应在同一顺序是snps行
参数：snp.data
An object of class "snp.matrix" containing the SNP genotypes to be tested
一个类的对象"snp.matrix"包含的SNP基因型进行测试
参数：subset
A vector or expression describing the subset of subjects to be used in teh analysis. This is evaluated in the same environment as the phenotype and stratum arguments
一个向量或表达描述在格兰分析科目的子集。 phenotype和stratum参数，这是在同样的环境评价
参数：snp.subset
A vector describing the subset of SNPs to be considered. Default action is to test all SNPs.
一个向量描述的SNPs的子集加以考虑。默认动作是测试所有的SNPs。
Details
详情----------Details----------
Formally, the test statistics are score tests for generalized linear models with canonical link. That is, they are inner products between genotype indicators and the deviations of phenotypes from their stratum means. Variances (and covariances) are those of the permutation distribution obtained by randomly permuting phenotype within stratum.
正式，检验统计量是广义线性模型与典型环节的得分测试。也就是说，他们是从地层的手段，其表型的基因型指标和偏差之间的内在产品。地层内的表型随机置换获得的排列分布的差异（方差）。
The subset argument can either be a logical vector of length equal to the length of the vector of phenotypes, an integer vector specifying positions in the data frame, or a character vector containing names of the selected rows in the data frame. Similarly, the snp.subset argument can be a logical, integer, or character vector.
subset参数可以是一个逻辑向量的长度等于表型矢量的长度，整数向量，指定data框架，包含所选行的名称或特征向量的位置data框架。同样，snp.subset参数可以是一个逻辑，整数或字符的向量。
值----------Value----------
A dataframe, with columns
与列dataframe，
参数：chi2.1df
Cochran-Armitage type test for additive genetic component
科克伦 - 阿米蒂奇添加剂遗传组成部分的型式试验
参数：chi2.2df
Chi-squared test for both additive and dominance components
卡方检验，添加剂和优势组件
参数：N
The number of valid data points used
使用有效的数据点的数量
注意----------Note----------
The behaviour of this function for objects of class X.snp.matrix is as described by Clayton (2008). Males are treated as homozygous females and corrected variance estimates are used.
这个函数的行为为X.snp.matrix类的对象被描述为克莱顿（2008年）。为纯合子的女性和校正方差估计治疗男性使用。
作者（S）----------Author(s)----------
David Clayton <a href="mailto:david.clayton@cimr.cam.ac.uk">david.clayton@cimr.cam.ac.uk</a>
参考文献----------References----------
参见----------See Also----------
snp.lhs.tests, snp.rhs.tests
snp.lhs.tests，snp.rhs.tests
举例----------Examples----------
data(testdata)
results <- single.snp.tests(cc, stratum=region, data=subject.data,
snp.data=Autosomes, snp.subset=1:10)
summary(results)
# QQ plot - see \code{\link{qq.chisq}}[QQ图 - 看\代码{\链接{qq.chisq}的}]
qq.chisq(results$chi2.1df)
qq.chisq(results$chi2.2df)
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 2012-2-25 15:00:47
