read.plink(snpStats)
read.plink()所属R语言包：snpStats
Read a PLINK binary data file as a SnpMatrix
1 SnpMatrix阅读砰砰二进制数据文件
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The package PLINK saves genome-wide association data in groups of three files, with the extensions .bed, .bim, and .fam. This function reads these files and creates an object of class "SnpMatrix"
砰砰的包保存在三个文件组的全基因组关联数据，扩展.bed，.bim，.fam。该函数读取这些文件，并创建一个对象类"SnpMatrix"
用法----------Usage----------
read.plink(bed, bim, fam, na.strings = c("0", "-9"), sep = "." , select.subjects = NULL, select.snps = NULL)
参数----------Arguments----------
参数：bed
The name of the file containing the packed binary SNP genotype data. It should have the extension .bed; if it doesn't, then this extension will be appended
包含打包的二进制SNP基因型数据文件的名称。它应该有扩展.bed;如果没有，那么这个扩展将追加
参数：bim
The file containing the SNP descriptions
该文件包含的SNP描述
参数：fam
The file containing subject (and, possibly, family) identifiers. This is basically a tab-delimited "pedfile"
该文件包含主题（以及可能的话，家庭）标识符。这基本上是一个制表符分隔“pedfile”
参数：na.strings
Strings in .bam and .fam files to be recoded as NA
在字符串中。BAM。FAM文件重新编码为NA
参数：sep
A separator character for constructing unique subject identifiers
一个独特的主题标识符建设的分隔符
参数：select.subjects
A numeric vector indicating a subset of subjects to be selected from the input file (see details)
一个数值向量表示科目的一个子集，从输入文件选择（见详情）
参数：select.snps
Either a numeric or a character vector indicating a subset of SNPs to be selected from the input file (see details)
无论是数字或字符向量表明单核苷酸多态性的一个子集，从输入文件选择（见详情）
Details
详情----------Details----------
If the bed argument does not contain a filename with the file extension .bed, then this extension is appended to the argument. The remaining two arguments are optional; their default values are obtained by replacing the .bed filename extension by .bim and .fam respectively. See the PLINK documentation for the detailed specification of these files.
如果bed参数不包含文件名，文件扩展名.bed，然后这个扩展附加的说法。剩下的两个参数是可选的;取代.bed文件扩展名.bim和.fam分别获得它们的默认值。对这些文件的详细规格，请参阅的砰砰文件。
The select.subjects or select.snps argument can be used to read a subset of the data. Use of select.snps requires that the .bed file is in SNP-major order (the default in PLINK). Likewise, use of select.snps requires that the .bed file is in individual-major order. Subjects are selected by their numeric order in the PLINK files, while SNPs are selected either by order or by name. Note that the order of selected SNPs/subjects in the output objects will be the same as their order in the PLINK files.
select.subjects或select.snps参数，可以用来读取数据的一个子集。使用select.snps要求.bed文件SNP主要为了（砰砰默认）。同样，使用select.snps要求.bed文件中个别大订单。他们在砰砰文件的数字顺序选择的主题，而SNPs是选择或名称。请注意，选定的SNPs /输出对象主体的顺序将是他们在砰砰文件的顺序相同。
Row names for the output SnpMatrix object and for the accompanying subject description dataframe are taken as the pedigree identifiers, when these provide the required unique identifiers. When these are duplicated, an attempt is made to use the pedigree-member identifiers instead but, when these too are duplicated, row names are obtained by concatenating, with a separator character, the pedigree and pedigree-member identifiers.
输出SnpMatrix对象和随附的主题描述dataframe的行名谱系标识符，当这些提供所需的唯一标识符。当这些被复制，企图血统成员的标识符，而不是使用，但，当这些重复行名称通过连接，分隔符，谱系和血统成员的标识符。
值----------Value----------
A list with three elements:
一个具有三个元素的列表：
参数：genotypes
The output genotype data as an object of class
作为一个类的对象的输出基因型数据
"SnpMatrix".
"SnpMatrix"。
参数：fam
A dataframe corresponding to the .fam file, containing the first six fields in a standard pedfile. The row names will correspond with those of the SnpMatrix
一个dataframe对应.fam文件，包含第一六个在标准pedfile领域的。该行的名称将对应与SnpMatrix的
参数：map
A dataframe correponding to the .bim file. the row names correpond with the column names of the SnpMatrix
一个dataframe correponding到.bim文件。 SnpMatrix列名的列名correpond
注意----------Note----------
No special provision is made to read XSnpMatrix objects; such data should first be read as a SnpMatrix and then coerced to an XSnpMatrix using new or as.
没有特殊的规定是由读取XSnpMatrix对象，这样的数据，首先应读为1 SnpMatrix然后强迫XSnpMatrix用new或as。
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----------
http://pngu.mgh.harvard.edu/~purcell/plink/
参见----------See Also----------
write.plink,
write.plink
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 14:46:27
