ped2geno(trio)
ped2geno()所属R语言包：trio
Transformation of Ped-File
转型的PED文件
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Transforms a ped-file into a genotype file as required by, e.g., the functions for computing the genotypic TDT.
到的基因型文件变换一个路人文件所要求的，例如，函数用于计算的基因型的TDT。
用法----------Usage----------
ped2geno(ped, snpnames = NULL, coded = c("12", "AB", "ATCG", "1234"),
naVal = 0, cols4ID = FALSE)
参数----------Arguments----------
参数：ped
a data frame in ped format, i.e. the first six columns must contain information on the families as typically presenteed in ped files, where the column names of these six columns must be "famid", "pid", "fatid", "motid", "sex","affected". The last two of these six columns are ignored. The IDs of individuals in the second column must be unique (not only within the family, but among all individuals). The columns following the six columns are assumed to contain the alleles of the SNPs, where the alleles are coded using the letters/numbers in coded, and missing values are coded by naVal. Thus, the seventh and the eigth column contain the two alleles for the first SNP, the ninth and tenth the two alleles for the second SNP, and so on. Contrary to the names of the first six columns, the names of the columns representing the SNPs are ignored, and SNP names can be specified using snpnames.
一个数据框在PED的格式，即第一列必须包含在的PED文件，这六列的列名必须是“famid”，“PID”，“fatid”的家庭通常presenteed， “MOTID”，“性别”，“影响”。这六个列的最后两个被忽略。个人在第二列中的ID必须是唯一的（不仅是在家庭内，但在所有个人）。假设六列的列包含的等位基因的单核苷酸多态性，等位基因编码的字母/数字coded，缺失值编码naVal。因此，第七和第八个列包含的两个等位基因为第一SNP，第九和第十的两个等位基因的第二个SNP，等。的前六列的名称，代表的单核苷酸多态性的列的名字将被忽略，并且可以指定使用snpnamesSNP的名字。
参数：snpnames
a character vector containing the names of the SNPs. If not specified, generic names are assigned (i.e. SNP1, SNP2, ...). Ignored if ped just contains one SNPs.
字符向量的单核苷酸多态性的名字。如果未指定，通用名分配（即SNP1，SNP2，...）。如果忽略ped只包含一个单核苷酸多态性。
参数：coded
the coding used for the alleles of the SNPs. coded = "12", e.g., means that one of the alleles is coded by 1, and the other by 0. coded = "ATCG" means that the alleles are coded by the actual base.
所使用的编码的基因的单核苷酸多态性。 coded = "12"，例如，指，一个等位基因之一的是，由1编码，和其他由0。 coded = "ATCG"意味着该等位基因编码的实际基。
参数：naVal
the value used for specifying missing values.
所使用的值指定缺少值。
参数：cols4ID
logical indicating whether columns should be added to output matrix containing the family ID and the individual ID. If FALSE, the individual IDs are used as the row names of the output matrix.
逻辑指示是否应该被添加到输出矩阵包含家庭ID和个别ID列。如果FALSE，个别的ID作为输出矩阵的行的名称。
值----------Value----------
A vector (if ped consists of alleles for one SNP) or matrix (otherwise) containing one column for each SNP representing the genotypes of the respective SNP, where the genotypes are coded by 0, 1, 2 (i.e. the number of minor alleles), and missing values are represented by NA. The vector or matrix contains 3 * t values for each SNP genotyped at the t trios, where each block of 3 values is composed of the genotypes of the father, the mother, and the offspring (in this order) of a specific trio. If data for a family with more than one children are available, each of the children is treated as a separate trio.
的向量（如果ped的等位基因组成一个SNP）或矩阵（否则）包含一列的每个SNP代表各自的SNP的基因型，其中基因型编码的0，1，2（即数字次要等位基因），缺失值表示NA。向量或矩阵的包含3 * t的值每个SNP基因分型在t“三重奏，每块3的值是由基因型的父亲，母亲和后代（按照这个顺序）的特定三人。如果数据有一个以上孩子的家庭，每个孩子被视为一个独立的三人。
（作者）----------Author(s)----------
Holger Schwender, <a href="mailto:holger.schwender@udo.edu">holger.schwender@udo.edu</a>
参见----------See Also----------
tdt, tdt2way, trio.check
tdt，tdt2way，trio.check
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 2012-10-1 12:05:58
