R语言 scrime包 colEpistatic()函数中文帮助文档(中英文对照)

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colEpistatic(scrime)
colEpistatic()所属R语言包：scrime

                                        Cordell's Test for Epistatic Interactions
                                         科德尔的测试上位相互作用

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Performs the likelihood ratio test for epistatic interactions proposed by Cordell (2002) for case-control data, where colEpistatic assumes that each column represents a SNP, and rowEpistatic assumes that each row represents a SNP.
执行上位科德尔（2002）提出的情况下，控制数据的交互，似然比检验colEpistatic假设每一列代表一个SNP，和rowEpistatic假设每一行代表一个SNP。


用法----------Usage----------


colEpistatic(mat.snp, cl, genes = NULL, warnError = TRUE)
rowEpistatic(mat.snp, cl, genes = NULL, warnError = TRUE)

## S3 method for class 'colEpi'
print(x, top = 5, digits = 4, ...)



参数----------Arguments----------

参数：mat.snp
a matrix containing genotype data, where the genotypes of each SNPs need to be coded by the number of minor alleles, i.e. 0, 1, and 2. Missing values are allowed. For colEpistatic, each column of mat.snp is assumed to represent a SNP, and each row a subject. For rowEpistatic, each row of mat.snp is assumed to represent a subject, and each column a SNP.  
一个矩阵包含基因型数据，其中由次要等位基因的数目，即0，1，和2需要被编码的各单核苷酸多态性的基因型。遗漏值是允许的。对于colEpistatic，每一列mat.snp被认为代表SNP，每行一个主题。对于rowEpistaticmat.snp假设为代表的主题，每列一个SNP，每行。


参数：cl
a numeric vector of ones and zeros specifying which of the subjects in mat.snp are cases (coded by 1) and which are controls (coded by 0).
指定的科目的1和0的数字矢量mat.snp的情况（1编码）和对照组（编码为0）。


参数：genes
a character vector containing the names of the genes (or, e.g., LD-blocks or pathways) to which the SNPs belong. If specified,  only the two-way interactions between SNPs from different genetic sets (e.g., genes, LD-blocks, or pathways) are tested.  If NULL, all two-way interactions between all possible pairs of SNPs are tested.
包含名称的基因（或者，例如，LD-块或通路）的SNPs属于一个字符矢量。如果指定了，只有单核苷酸多态性之间的双向互动，从不同的基因组（例如，基因，LD块，或途径）进行测试。如果NULL，对所有可能的SNP位点之间的双向互动测试。


参数：warnError
logical indicating whether the statistics for the gTDT for pairs of SNPs should be returned as NA if the fitting  of one of the logistic regression models with glm returns warning. If warnError = FALSE,  these warnings will be ignored, and the gTDT will be performed also for these SNP pairs.
逻辑是否应退还的统计数据，对单核苷酸多态性的gTDT NA，如果Logistic回归模型的拟合一个glm返回的警告。如果warnError = FALSE，这些警告将被忽略，并将进行的gTDT，也为这些SNP对。


参数：x
an object of class colEpi, i.e. the output of either colEpistatic or rowEpistatic.
类的一个对象colEpi是colEpistatic或rowEpistatic，即输出。


参数：top
number of interactions that should be printed. If top is set to 0 or 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 (sorted by their p-values).
应该打印的交互数。如果top被设置成0或相互作用的数量是小于或等于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相互作用的最小的P值打印（P-值排序）。


参数：digits
number of digits that should be printed.
应打印的数字。


参数：...
ignored.
忽略不计。


值----------Value----------

An object of class colEpi consisting of <table summary="R valueblock"> <tr valign="top"><td>ll.main</td> <td> a numeric vector containing the values of the maximized loglikelihoods of the logistic regression models  considering only main effects,</td></tr> <tr valign="top"><td>ll.full</td> <td> a numeric vector containing the values the maximized loglikelihoods of the logistic regression models additionally  containing interaction terms,</td></tr> <tr valign="top"><td>stat</td> <td> a vector comprising the values of the test statistic,</td></tr> <tr valign="top"><td>pval</td> <td> a vector comprising the corresponding p-values,</td></tr> <tr valign="top"><td>genes</td> <td> if genes has been specified, a vector composed of the gene pairs to which the SNP pairs belong,</td></tr> <tr valign="top"><td>vec.error</td> <td> if warnError = TRUE, a list in which an entry corresponding to a SNP pair for which the fitting of (at least) one of the logistic regression models led to a warning shows this warning message of glm, and all other entries are NULL.</td></tr> </table>
类的一个对象colEpi组成的<table summary="R valueblock"> <tr valign="top"> <TD> ll.main</ TD> <td>一个数字向量的值logistic回归模型只考虑主要影响的的最大化loglikelihoods的，</ TD> </ TR> <tr valign="top"> <TD>ll.full </ TD> <td>一个数字向量的值Logistic回归模型中还含有交互作用项，</ TD> </ TR> <tr valign="top"> <TD>stat </ TD> <td>一个向量，它含有的值的的最大化loglikelihoods的检验统计量，</ TD> </ TR> <tr valign="top"> <TD> pval </ TD> <td>一个向量，其特征在于它包括相应的p值</ TD> </ TR> <tr valign="top"> <TD> genes </ TD> <TD>如果genes已指定，矢量组成的基因组的SNP对属于< / TD> </ TR> <tr valign="top"> <TD> vec.error </ TD> <TD>如果warnError = TRUE，一个列表，其中一个SNP对对应的条目配件（至少）一个Logistic回归模型的警告显示此警告消息的glm，和其他所有条目都是NULL。</ TD> </ TR> </表>


（作者）----------Author(s)----------



Holger Schwender, <a href="mailto:holger.schwender@udo.edu">holger.schwender@udo.edu</a>




参考文献----------References----------

Cordell, H. J. (2002). Epistasis: What it Means, what it Doesn't mean, and Statistical Methods to Detect it in Humans. Human Molecular Genetics, 11, 2463-2468.

参见----------See Also----------

colTDT2way
colTDT2way

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


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