R语言 chopsticks包 read.snps.pedfile()函数中文帮助文档(中英文对照)

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read.snps.pedfile(chopsticks)
read.snps.pedfile()所属R语言包：chopsticks

                                        Read genotype data from  a LINKAGE "pedfile"
                                         基因型数据从联动“pedfile”

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This function reads data arranged as a LINKAGE "pedfile" with some restrictions and returns a list of three objects: a data frame containing the initial 6 fields giving pedigree structure, sex and disease status, a vector or a data frame containing snp assignment and possibly other snp infomation, and an object of class "snp.matrix" or "X.snp.matrix" containing the genotype data
此功能读取数据：“pedfile”有一些限制和回报三个对象名单作为联系安排一个数据框包含在最初的6个领域给予谱系结构，性别和疾病状态，一个向量或一个数据框，含有SNP分配的，并其他可能的SNP当前和对象类"snp.matrix"或"X.snp.matrix"包含的基因型数据


用法----------Usage----------


read.snps.pedfile(file, snp.names=NULL, assign=NULL, missing=NULL, X=FALSE, sep=".", low.mem = FALSE)



参数----------Arguments----------

参数：file
The file name for the input pedfile
为输入pedfile文件名


参数：snp.names
A character vector giving the SNP names. If an accompanying map file or an info file is present, it will be read and the information used for the SNP names, and also the information merged with the result. If absent, the SNPs will be named numerically ("1", "2", ...)
字符向量的SNP名称。如果所附的图文件或信息文件是存在的，它将会读取和SNP的名称使用的信息，信息合并的结果。如果缺席，单核苷酸多态性将被命名为数字（“1”，“2”，...）


参数：assign
A list of named mappings for which letter maps to which Allele; planned for the future, not currently used  
一个命名为字母映射到的等位基因的映射列表;对未来的计划，而不是目前使用的


参数：missing
Meant to be a single character giving the code recorded for alleles of missing genotypes ; not used in the current code
意思是一个单一的字符，给予缺失基因型的等位基因记录的代码;在当前代码未使用


参数：X
If TRUE the pedfile is assumed to describe loci on the X chromosome
如果TRUE：pedfile是假设来描述X染色体上的基因位点


参数：sep
The character separating the family and member identifiers in the constructed row names; not used
字符分隔在建行名家庭成员的标识符;不使用


参数：low.mem
Switch over to input with a routine which requires less memory to run, but takes a little longer. This option also has the disadvantage that assignment of A/B genotype is somewhat non-deterministic and depends  the listed order of samples.
切换到输入与常规需要较少的内存来运行，但需要时间长一些。此选项也有缺点的A / B型的任务是有点非确定性，取决于上市的样品顺序。


Details

详情----------Details----------

Input variables are assumed to take the usual codes, with the restriction that the family (or pedigree) identifiers will be held as strings, but identifiers for members within families must be coded as integers. Genotype should be coded as pairs of single character allele codes (which can be alphameric or numeric), from either 'A', 'C', 'G', 'T' or '1', '2', '3', '4', with 'N', '-' and '0' denoting a missing; everything else is considered invalid and would invalidate the whole snp; also more than 2 alleles also cause the snp to be marked invalid.
输入变量的假设与限制，家庭（或血统）的标识符将作为字符串举行通常的代码，但在家庭成员的标识符必须为整数编码。应编码为基因型对单字符的等位基因代码（可以是字母数字或数字），无论从“A”，“C”，“G”，T或1，2，3， 4，与“N， - 和0表示丢失;一切被视为无效，并会失效，整个SNP也超过2个等位基因也导致SNP被标记为无效。

Row names of the output objects are constructed by concatenation of the pedigree and member identifiers, "Family", "Individual" joined by ".", e.g. "Family.Adams.Individual.0".
输出对象的行名串联的血统和成员标识符，“家庭”，“个人”加入了“构建”，例如： “Family.Adams.Individual.0”。


值----------Value----------


参数：snps
The output "snp.matrix" or "X.snp.matrix"
输出"snp.matrix"或"X.snp.matrix"


参数：subject.support
A data frame containing the first six fields of the pedfile
一个数据框包含的上半年的pedfile的领域


作者（S）----------Author(s)----------


Hin-Tak Leung



参见----------See Also----------

snp.matrix-class, X.snp.matrix-class, read.snps.long, read.HapMap.data,
snp.matrix-class，X.snp.matrix-class，read.snps.long，read.HapMap.data

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


注：
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