ld(snpStats)
ld()所属R语言包：snpStats
Pairwise linkage disequilibrium measures
两连锁不平衡的措施
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function calculates measures of linkage disequilibrium between pairs of SNPs. The two SNPs in each pair may both come from the same SnpMatrix object, or from two different SnpMatrix objects. Statistics which can be calculated are the log likelihood ratio, odds ratio, Yule's Q, covariance, D-prime, R-squared, and R.
此函数计算的SNP对之间的连锁不平衡的措施。每对中的两个单核苷酸多态性可能都来自相同的SnpMatrix对象，或从两个不同的SnpMatrix对象。可以计算的统计数据对数似然比，胜算比，尤尔的Q，协方差，D首要，R-平方，和R.
用法----------Usage----------
ld(x, y = NULL, depth = NULL, stats, symmetric = FALSE)
参数----------Arguments----------
参数：x
An object of class SnpMatrix or XSnpMatrix
一个对象类SnpMatrix或XSnpMatrix
参数：y
(Optional) Another object of the same class as x. If y is supplied, LD statistics are calculated between each column of x and each column of y. Otherwise, they are calculated between columns of x
（可选）为x同一类的另一个对象。如果y提供，劳工处统计计算每个列，每个列xy之间。否则，他们之间的计算列x
参数：depth
When y is not supplied, this parameter is mandatory and controls the maximum lag between columns of x considered. Thus, LD statistics are calculated between x[,i] and x[,j] only if i and j differ by no more than depth
当y没有提供，这个参数是强制性控制x考虑的列之间的最大的滞后。因此，劳工处统计计算之间x[,i]和x[,j]只有i和j没有比depth不同
参数：stats
A character vector specifying the linkage disequilibrium measures to be calculated. This should contain one or more of the strings: "LLR", "OR", "Q", "Covar", "D.prime", "R.squared", ad "R"
要计算一个指定的连锁不平衡的特征向量措施。这应该包含一个或多个字符串："LLR"，"OR"，"Q"，"Covar"，"D.prime"，"R.squared"，广告<X >
参数：symmetric
When no y argument is supplied this argument controls the format of the output band matrices. If TRUE, symmetric matrices are returned and, otherwise, an upper triangular matrices are returned
当没有y参数提供此参数控制输出带状矩阵的格式。 TRUE如果，对称矩阵返回，否则返回一个上三角矩阵
Details
详情----------Details----------
For each pair of SNPs, phased haplotype frequencies are first estimated by maximum likelihood using the method described by Clayton and Leung (2007). The arrays of chosen LD statistics are then calculated and returned, either as band matrices (when y is not supplied), or as conventional rectangular matrices (when y is supplied). Band matrices are stored in compressed form as objects of class dsCMatrix (symmetric) or dgCMatrix (upper triangular). These classes are defined in the "Matrix" package)
对于每单核苷酸多态性，分阶段的单体型频率估计使用克莱顿和亮（2007）所描述的方法的可能性最大。挑选劳工处统计的阵列，然后计算返回，无论是作为带状矩阵（当y不提供），或作为传统的长方矩阵（当y提供）。带状矩阵压缩形式存储在作为类对象dsCMatrix（对称）或dgCMatrix（上三角）。这些类中定义的"Matrix"包）
值----------Value----------
If only one LD statistic is requested, the function returns either a matrix or a compressed band matrix. If more than one LD statistic is requested, a list of such objects is returned
如果只有一个劳工处统计的要求，该函数返回一个矩阵或压缩带矩阵。如果多个LD统计的要求，这些对象的列表返回
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----------
(this paper is included in package documentation)
参见----------See Also----------
"Matrix-class"
"Matrix-class"
举例----------Examples----------
data(testdata)
ld1 <- ld(Autosomes[, 1:50], depth=10, stats=c("D.prime", "R.squared"))
ld2 <- ld(Autosomes[, 1:20], Autosomes[, 21:25], stats="R.squared")
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 2012-2-26 14:44:29
