rowTrendFuzzy(scrime)
rowTrendFuzzy()所属R语言包：scrime
Trend Test for Fuzzy Genotype Calls
趋势的模糊基因型分型测试
译者：生物统计家园网 机器人LoveR
描述----------Description----------
rowTrendFuzzy performs the trend test proposed by Louis et al. (2010) based on fuzzy genotype calls, i.e. the weighted sums over the confidences for the three genotypes as they are determined by preprocessing algorithms (e.g., CRLMM) or imputation procedures.
rowTrendFuzzy进行趋势检验，路易斯等人提出的。 （2010）基于模糊基因型分型，即加权和三种基因型的信心，因为他们是由的预处理算法（例如，CRLMM）或插补程序。
Given the confidences and scores for all three genotypes, getMatFuzzy constructs a matrix containing the fuzzy genotype calls.
所有三种基因型的信心和分数，getMatFuzzy构造矩阵的模糊基因型分型。
用法----------Usage----------
rowTrendFuzzy(score, probs, y, mat.fuzzy = NULL, alternative = c("two.sided", "less", "greater"),
check = TRUE)
getMatFuzzy(score, probs, check = TRUE)
参数----------Arguments----------
参数：score
either a numeric vector of length 2 or 3, or a character string.
可以是数字型的矢量的长度为2或3，或者是一个字符串。
If the latter, score must be either "additive", "dominant", "recessive", or an abbreviation of these terms. If score = "additive", then score is set to c(0, 1, 2). If score = "dominant", then score is set to c(0, 1, 1). And if score = "recessive", score is set to c(0, 0, 1).
如果是后者，score是"additive"，"dominant"，"recessive"，或这些术语的缩写。如果score = "additive"，那么score设置为c(0, 1, 2)。如果score = "dominant"，那么score设置为c(0, 1, 1)。如果score = "recessive"，score设置为c(0, 0, 1)。
If score is a numeric vector of length 2, then the first value must be the score for the heterozygous genotype, and the second value the score for the homozygous variant genotype. If score is of length, the first entry of this vector must be a zero (the score for the homozygous reference genotype), followed by the scores for the heterozygous and homozygous variant genotype.
如果score是一个数值向量的长度为2，那么第一个值必须为杂合子基因型的得分，而第二个值的得分为纯合子的基因型。如果score是长度，此向量的第一个条目必须是一个零（为的纯合子参考基因型的得分），其次由杂合子和纯合子的基因型的分数。
参数：probs
a list of length 2 or 3 consisting of matrices of the same size. Each matrix must contain the confidences for one of the three genotypes, where each row in the matrix represents a SNP and each column a sample (which must be in the same order in all matrices). The matrices in probs correspond to the scores in score. Thus, if probs has length 2, then the first matrix must contain the confidences for the heterozygous genotype, and the second matrix the confidences for the homozygous variant genotype. All elementwise sums of these two matrices must be smaller than or equal to 1. If probs has length 3, the first object must be a matrix containing the confidences for the homozygous reference genotype, followed by the two other matrices comprising the confidences for the heterozygous and homozygous variant genotype. All elementwise sums of the three matrices must be equal to 1.
长度为2或3个相同大小的矩阵组成的列表。每个矩阵必须包含的置信度的3种基因型，其中矩阵中的每一行代表一个SNP和每一列的样品（其中必须以相同的顺序在所有矩阵）之一。 probs矩阵对应的分数在score。因此，如果probs具有长度为2，然后在第一矩阵必须包含的杂合基因型中，和第二矩阵的纯合子的基因型的置信度的置信度。所有的elementwise大笔这两个矩阵必须是小于或等于1。如果probs有长度为3时，所述第一对象必须是含有的置信度为纯合子的参考的基因型，随后由包括以下为杂合子和纯合子的基因型的置信度的其他两个矩阵的矩阵。的三个矩阵的所有的elementwise款项必须等于1。
参数：y
a vector of zeros and ones specifying which of the samples in the matrices in probs are cases (1) and which are controls (0).
零和一指定的样品中的矩阵中的矢量probs的情况（1），哪些是控制（0）。
参数：mat.fuzzy
a matrix containing the fuzzy genotype calls. If specified, score and probs are not allowed to be specified in rowTrendFuzzy. If NULL, mat.fuzzy is determined by employing getMatFuzzy, i.e.\ by multiplying the confidences in probs with the corresponding scores in score and computing the elementwise sums over the resulting matrices with the weighted confidences.
矩阵的模糊基因型分型。如果指定的话，score和probs是不允许被指定在rowTrendFuzzy。如果NULL，mat.fuzzy决定采用getMatFuzzy，即\乘以信心probsscore，和计算来说，elementwise的款项中相应的分数超过所得到的矩阵的加权的置信度。
参数：alternative
a character string specifying the alternative hypothesis. Must be one of "two.sided" (default), "greater", or "less". Abbreviations (e.g.\ the initial letter) for these choices are also allowed.
一个字符串指定其他假设。必须是"two.sided"（默认），"greater"或"less"。这些选择的缩写（例如：\的首字母）也是允许的。
参数：check
logical specifying whether the specified objects should be extensively checked. If FALSE, only some basic checks are done. It is highly recommended to use check = TRUE, although the checking takes much more computing time than the determination of the values of the trend test statistic.
逻辑指定是否应广泛检查指定的对象。如果FALSE，只有一些基本的检查都做了。我们强烈建议使用check = TRUE，虽然检查需要更多的计算时间比测定的趋势检验统计量的值。
值----------Value----------
For getMatFuzzy, a matrix containing the fuzzy genotype calls. For rowTrendFuzzy, a list consisting of <table summary="R valueblock"> <tr valign="top"><td>stat</td> <td> a vector containing the values of the trend test statistic for all SNPs comprised by probs,</td></tr> <tr valign="top"><td>rawp</td> <td> a vector containing the unadjusted p-values computed for the values in stat based on a standard normal distribution and the specification of alternative.</td></tr> <tr valign="top"><td>theta</td> <td> a vector containing estimates for the log odds ratios for risk corresponding to stat,</td></tr> <tr valign="top"><td>varTheta</td> <td> a vector containing the variance estimates for theta.</td></tr> </table>
getMatFuzzy，矩阵包含模糊基因型调用。 rowTrendFuzzy，由<table summary="R valueblock"> <tr valign="top"> <TD> stat</ TD> <td>一个向量的值的列表中趋势检验统计量的所有SNP位点组成probs，</ TD> </ TR> <tr valign="top"> <TD> rawp </ TD> <td>一个向量包含未调整p-值计算出的值stat标准正态分布和规范的基础上，alternative。</ TD> </ TR> <tr valign="top"> <TD>theta </ TD> <TD>一个向量，包含log的比值比相应的风险估计stat“</ TD> </ TR> <tr valign="top"> <TD> X> </ TD> <TD>一个向量，包含的方差估计varTheta。</ TD> </ TR> </表>
参考文献----------References----------
Louis, T.A., Carvalho, B.S., Fallin, M.D., Irizarry, R.A., Li, Q., and Ruczinski, I. (2010). Association Tests that Accommodate Genotyping Errors. In Bernardo, J.M., Bayarri, M.J., Berger, J.O., Dawid, A.P., Heckerman, D., Smith, A.F.M., and West, M. (eds.), Bayesian Statistics 9, 393-420. Oxford University Press, Oxford, UK. With Discussion.
参见----------See Also----------
rowTrendStats, rowCATTs
rowTrendStats，rowCATTs
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。
|
发表于 2012-9-29 23:04:25
