read.snps.long.old(chopsticks)
read.snps.long.old()所属R语言包：chopsticks
Read SNP input data in "long" format (old version)
SNP输入数据读“长”格式（旧版本）
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function reads SNP genotype data and creates an object of class "snp.matrix" or "X.snp.matrix". Input data are assumed to be arranged as one line per SNP-call (without any headers). This function can read gzipped files.
此功能读取SNP基因型数据，并创建了一个对象类"snp.matrix"或"X.snp.matrix"。假设要输入的数据为一体的每个SNP呼叫线（无头）排列。此功能可以读取gzip文件。
用法----------Usage----------
read.snps.long.old(file, chip.id, snp.id, codes, female,
conf = 1, threshold = 0.9, drop=FALSE,
sorted=FALSE, progress=interactive())
参数----------Arguments----------
参数：file
Name of file containing the input data. Input files which have been compressed by the gzip utility are recognized
文件名包含输入数据。确认输入gzip实用已压缩文件
参数：chip.id
Array of type "character" containing (unique) identifiers for the chips, samples, or subjects for which calls are to be read. Other samples in the input data will be ignored
数组的类型"character"含（唯一）标识符的呼叫要读取的芯片，样品，或科目。其他样本在输入数据将被忽略
参数：snp.id
Array of type "character" containing (unique) identifiers of the SNPs for which data will be read. Again, further SNPs in the input data will be ignored
数组类型"character"含（唯一）的SNP数据将被读取的标识符。再次，进一步在输入数据的SNPs将被忽略
参数：codes
For autosomal SNPs, an array of length 3 giving the codes for the three genotypes, in the order homozygous(AA), heterozygous(AB), homozygous(BB). For X SNPs, an additional two codes for the male genotypes (AY and BY) must be supplied. All other codes will be treated as "no call". The default codes are "0", "1", "2" [,"0", "2"]
为常染色体单核苷酸多态性，长度为3的数组提供三种基因型的代码，在为了纯合子（AA），杂合子（AB），纯合子（BB）。为X个SNPs，另外两名男性的基因型（AY和BY）代码必须提供。所有其他的代码将被视为“不呼叫”。默认代码"0"，"1"，"2"，"0"，"2"]
参数：female
If the data to be read refer to SNPs on the X chromosome, this argument must be supplied and should indicate whether each row of data refers to a female (TRUE) or to a male (FALSE). The output object will then be of class "X.snp.matrix".
如果要读取的数据是指在X染色体上的单核苷酸多态性，这种说法必须提供并应说明是否每一行数据，是指一个女（TRUE）或男性（FALSE）。然后将输出对象的类"X.snp.matrix"。
参数：conf
Confidence score. See details
信心得分。查看详情
参数：drop
If TRUE, any rows or columns without genotype calls will be dropped from the output matrix. Otherwise the full matrix, with rows and columns defined by the chip.id and snp.id arguments, will be returned
如果TRUE，任何行或无基因型分型列将输出矩阵下降。否则，全矩阵，定义chip.id和snp.id参数，将返回的行和列
参数：threshold
Acceptance threshold for confidence score
信心得分验收阈值
参数：sorted
Is input file already sorted into the correct order (see details)?
输入文件已经排序到正确的顺序（见详情）？
参数：progress
If TRUE, progress will be reported to the standard output stream
如果TRUE，进度将上报到标准输出流
Details
详情----------Details----------
Data are assumed to be input with one line per call, in free format:<br><br> <chip-id> <snp-id> <code for genotype call> [<confidence>] ... <br><br> Currently, any fields following the first three (or four) are ignored. If the argument sorted is TRUE, the file is assumed to be sorted with snp-id as primary key and chip-id as secondary key using the current locale. The rows and columns of the returned matrix will also be ordered in this manner. If sorted is set to FALSE, then an algorithm which avoids this assumption is used. The rows and columns of the returned matrix will then be in the same order as the input chip_id and snp_id vectors. Calls in which both id fields match elements in the chip.id and snp.id arguments are read in, after (optionally) checking that the level of confidence achieves a given threshold. Confidence level checking is controlled by the conf argument. conf=0 indicates that no confidence score is present and no checking is done. conf>0 indicates that calls with scores above threshold are accepted, while conf<0 indicates that only calls with scores below threshold should be accepted.
数据被认为是一行每次通话，在自由格式输入：参考参考<chip-id>的的基因型<snp-id> <code call>的[<confidence>] ...目前参考参考，任何领域继前三个（或四个）都将被忽略。如果参数sorted是TRUE，该文件被假定为与SNP-ID作为次要使用当前语言环境的关键芯片-ID作为主键和排序。返回矩阵的行和列也将在这种方式订购。如果sorted设置为FALSE，那么这个假设的算法，从而避免了使用。返回矩阵的行和列，然后将输入chip_idsnp_id向量，以相同的顺序。呼吁在这两个ID字段匹配的元素，在chip.id和snp.id参数阅读后，（可选）检查信心水平达到一个给定的阈值。置信水平检查conf参数控制。 conf=0表示没有信心的得分是目前并没有完成检查。 conf>0表示，，呼吁得分高于threshold接受，而conf<0表示分数低于threshold应接受的，只有检测。
The routine is case-sensitive and it is important that the <chip-id> and <snp-id> match the cases of chip.id and snp.id exactly.
常规是大小写敏感的，重要的是，的<chip-id>和<snp-id>chip.id和snp.id完全匹配的情况。
值----------Value----------
An object of class snp.matrix.
对象类snp.matrix。
注意----------Note----------
If more than one instance of any combination of chip_id element and snp_id element passes the confidence threshold, the called to be used is decided by the following rules:
如果多个实例的任何chip_id元素和snp_id元素传递的信心阈值，称为要使用的是由以下规则决定的组合：
1Any call trumps "no-call"
1Any呼叫王牌“呼叫”
2In the event of call conflict, "no-call" is returned
2英寸的呼叫冲突事件，“没有呼叫”返回
Use of sorted=TRUE is usually discouraged since the alternative algorithm is safer and, usually, not appreciably slower. However, if the input file is to be read multiple times and there is a reasonably close correspondence between cells of the matrix to be returned and lines of the input file, the sorted option can be faster.
sorted=TRUE由于替代算法是安全的，通常情况下，没有明显慢，通常不鼓励使用。然而，如果要读取输入文件多次，是要返回的矩阵和输入文件的行的单元之间有相当密切的对应关系，排序的选项可以更快。
This function has been replaced by the more flexible function read.snps.long.
此功能已被取代，更灵活的功能read.snps.long。
作者（S）----------Author(s)----------
David Clayton <a href="mailto:david.clayton@cimr.cam.ac.uk">david.clayton@cimr.cam.ac.uk</a> and Hin-Tak Leung
参考文献----------References----------
<h3>See Also</h3>
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 2012-2-25 15:00:06
