trio.prepare(trio)
trio.prepare()所属R语言包：trio
Generate Trio Data Format Suitable for Trio Logic Regression
生成适用于三重逻辑回归的的三重奏数据格式
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function transforms case-parent data into a format suitable as input for trio logic regression. The function can also be used for the imputation of missing genotypes in case-parent data,
此功能转换成合适的格式输入三人逻辑回归的情况下，父数据。功能也可用于归集的情况下，父数据丢失的基因型，
用法----------Usage----------
trio.prepare(trio.dat, freq=NULL, blocks=NULL, logic=TRUE, ...)
参数----------Arguments----------
参数：trio.dat
An object returned from the function trio.check.
返回的对象的功能trio.check。
参数：freq
An optional data frame specifying haplotype blocks and frequencies. For an example, see the data frame simuBkMap contained in this package. If provided, the following argument blocks will be ignored. The object must have three columns in the following order: block identifiers (key), haplotypes (hap), and haplotype frequencies (freq). The block identifiers must be unique for each block. For each block, the haplotypes must be encoded as a string of the integers 1 and 2, where 1 refers to the major allele and 2 refers to the minor allele. The respective haplotype frequencies will be normalized to sum one.
一个可选的数据框指定的单倍型块和频率。举一个例子，看到的数据框simuBkMap包含在此套件。如果提供的话，下面的参数blocks将被忽略。该对象必须有三列顺序如下：块标识符（key），单倍型（hap）和单倍型频率（freq）。每个块的块标识符必须是唯一的。对于每个块，必须被编码为一个字符串的整数1和2，其中1是指主要等位基因和2是指次要等位基因的单倍型。各自的单倍型频率将被标准化，总结1。
参数：blocks
An optional vector of integers, specifying (in sequence) the lengths of the linkage disequilibrium blocks. The sum of these integers must be equal to the total numbers of SNPs in the data set used as input. Using the integer 1 for SNPs not contained in LD blocks is required if this argument is used. If both arguments freq and blocks are NULL, complete linkage equilibrium is assumed (i.e., no correlation between the genotypes).
一个可选的矢量指定的整数，（按顺序）的连锁不平衡块的长度。这些整数的总和必须等于在用作输入的数据集的SNP位点的总数。如果使用该参数时，需要使用整数1个SNP位点不包含在LD块。如果两个参数freq和blocks是NULL，完整的连锁平衡假设（即，没有基因型之间的相关性）。
参数：logic
A logical value indicating whether the trio data are returned with genotypes in dominant and recessive coding, suitable as input for trio logic regression (TRUE), or if the imputed data should be returned in genotype format, using one variable per SNP (FALSE).
一个逻辑值，该值指示是否将三人返回的数据与基因型的显性和隐性的编码，适合作为输入三人逻辑回归（TRUE），或如果估算数据应使用一个变量，每SNP的基因型格式返回（FALSE“）。
参数：...
Optional arguments that can be passed to function haplo.em.
可选参数，可以传递给函数haplo.em。
Details
详细信息----------Details----------
To create the genotypes for the pseudo-controls it is necessary to take the LD structure of the SNPs into account. This requires information on the LD blocks. It is assumed that the user has already delineated the block structure according to his or her method of choice. The function trio.prepare, which operates on an output object of trio.check, accepts the block length information as an argument. If this argument is not specified, a uniform block length of 1 (i.e., no LD structure) is assumed. If the haplotype frequencies are not specified, they are estimated from the parents' genotypes using the function haplo.em. The function then returns a list that contains the genotype information in binary format, suitable as input for trio logic regression. Since trio logic regression requires complete data, the function trio.prepare also performs an imputation of the missing genotypes. The imputation is based on the estimated or supplied haplotype information.
要创建的基因型为伪控制，它是必要的，以考虑采取的SNPs LD结构。这需要的LD块的信息。假定用户已经划定的块结构，根据他或她的选择方法。函数trio.prepare，输出对象的trio.check，接受块长度信息作为参数。如果不指定该参数指定一个统一的块长度为1（即，没有LD结构）。如果未指定的单倍型频率，他们估计使用的功能haplo.em从父母的基因型。然后，该函数返回一个列表，其中包含二进制格式，适合作为输入三人逻辑回归的基因型信息。 ，由于三人逻辑回归需要完整的数据，功能trio.prepare也进行归集的缺失基因型。插补的基础上的估计或提供的单倍型信息。
值----------Value----------
参数：bin
A matrix suitable as input for trio logic regression. The first column specifies the cases and pseudo-controls as required by logic regression using conditional logistic regression (the integer 3 for the probands followed by three zeros indicating the pseudo-controls). The following columns specify the (possibly imputed) genotypes in dominant and recessive coding, with two binary variables for each SNP. This is returned only if logic = TRUE.
矩阵作为输入三人逻辑回归。第1列指定所要求的使用条件Logistic回归（整数后面的三个零，表明伪控制为先证者）的逻辑回归的情况下，伪控制。下面的列指定可能归咎于显性和隐性的编码，有两个二进制变量的每个SNP的基因型。这是只有logic = TRUE返回。
参数：trio
A data frame with imputed SNPs in genotype format derived from the input. This is returned only if logic = FALSE.
来自输入估算SNP位点的基因型格式的数据框。这是只有logic = FALSE返回。
参数：miss
A data frame with five columns indicating the missing genotypes in the input object. The five columns of the data frame refer to the family id (famid), the individual id (pid), the genotype (snp), the row numbers (r), and the column numbers (c). This element will be NULL if there are no missing data.
一个数据框有五列，在输入对象表示缺少的基因型。的五个列中的数据框是指家庭的id（famid），个别的id（pid），基因型（snp），行号码（r ）和列数（c）。此元素将NULL如果没有丢失的数据。
参数：freq
The estimated or supplied haplotype information, in the same format as described in the Arguments above.
的估计或供给的单倍型的信息，在上述“参数”中描述的相同的格式。
致谢----------Acknowledgments----------
Support was provided by NIH grants R01 DK061662 and HL090577.
由美国国立卫生研究院拨款：R01 DK061662和HL090577提供了支持。
（作者）----------Author(s)----------
Qing Li, mail2qing@yahoo.com
参考文献----------References----------
and Ruczinski, I. (2010). Detection of SNP-SNP Interactions in Trios of Parents with Schizophrenic Children. Genetic Epidemiology, 34, 396-406.
参见----------See Also----------
trio.check, haplo.em
trio.check，haplo.em
实例----------Examples----------
data(trio.data)
trio.tmp <- trio.check(dat=trio.ped1)
trio.bin <- trio.prepare(trio.dat=trio.tmp, blocks=c(1,4,2,3))
trio.bin$bin[1:8,]
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。
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发表于 2012-10-1 12:07:37
