RochePath-class(ShortRead)
RochePath-class()所属R语言包：ShortRead
"RochePath" class representing a Roche (454) experiment location
“RochePath”类代表罗氏（454）实验位置
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This class represents the directory location where Roche (454) result files (fasta sequences and qualities) can be found.
这个类表示罗氏（454）结果文件（FASTA序列和素质），可以发现该目录的位置。
类的对象----------Objects from the Class----------
Objects from the class are created with the RochePath constructor:
从类创建对象RochePath构造：
RochePath(experimentPath = NA_character_, readPath = experimentPath, qualPath = readPath, ..., verbose = FALSE)
RochePath(experimentPath = NA_character_, readPath = experimentPath, qualPath = readPath, ..., verbose = FALSE)
experimentPath character(1) or RochePath pointing to the top-level directory
experimentPathcharacter(1)或RochePath指向顶级目录
readPath character() of directories (typically in experimentPath) containing sequence (read) information. The default selects all directories matching
readPathcharacter()目录（通常experimentPath），包含序列信息（只读）。默认选择所有目录匹配
qualPath character() of directories (typically in experimentPath) containing quality information. The default selects all directories matching list.files(experimentPath,
qualPathcharacter()目录（通常在experimentPath）含高质量的信息。默认选择所有目录匹配：的<code> list.files（experimentPath的，
verbose logical(1) indicating whether invalid paths
详细logical(1)指示是否无效的路径
插槽----------Slots----------
RocheSet has the following slots:
RocheSet有以下插槽：
readPath: Object of class "character", as
readPath：Object类的"character"，作为
qualPath: Object of class "character", as
qualPath：Object类的"character"，作为
basePath: Object of class "character",
basePath：Object类的"character"，
延伸----------Extends----------
Class "ExperimentPath", directly. Class ".Roche", directly. Class ".ShortReadBase", by class "ExperimentPath", distance 2. Class ".ShortReadBase", by class ".Roche", distance 2.
类"ExperimentPath"，直接。类".Roche"，直接。类".ShortReadBase"，由类“ExperimentPath”，距离为2。类".ShortReadBase"“类”罗氏“，距离为2。
方法----------Methods----------
RochePath has the following methods or functions defined:
RochePath有以下几种方法或函数定义：
readFasta signature(dirPath = "RochePath", pattern=".\.fna$", sample = 1, run = 1, ...): Read sequences from files matching list.files(dirPath, pattern) (when dirPath="character") or list.files(readPath(dir)[run], pattern)[sample]. The
readFastasignature(dirPath = "RochePath", pattern=".\.fna$", sample = 1, run = 1, ...)：从匹配的文件读取序列list.files(dirPath, pattern)（dirPath="character"）list.files(readPath(dir)[run], pattern)[sample]。 “
readQual signature(dirPath = "RochePath", reads=NULL, pattern="\.qual$", sample=1, run=1, ...): Read quality scores from files matching list.files(qualPath(dirPath)[run])[sample]. Non-null reads is used as an (optional) template for parsing
readQualsignature(dirPath = "RochePath", reads=NULL, pattern="\.qual$", sample=1, run=1, ...)：读从匹配list.files(qualPath(dirPath)[run])[sample]文件的质量分数。非空reads被用作解析（可选）模板
readFastaQual signature(dirPath = "RochePath", fastaPattern = "\.fna$", qualPattern = "\.qual$", sample = 1, run = 1): read sequences and quality scores into a
readFastaQualsignature(dirPath = "RochePath", fastaPattern = "\.fna$", qualPattern = "\.qual$", sample = 1, run = 1)：读序列和质量分数成
readFastaQual signature(dirPath = "character", fastaPattern = "\.fna$", qualPattern = "\.qual$", sample = 1, run = 1): wrapper for method above, coercing dirPath
readFastaQualsignature(dirPath = "character", fastaPattern = "\.fna$", qualPattern = "\.qual$", sample = 1, run = 1)：上述方法的包装，强迫dirPath
readBaseQuality signature(dirPath = "RochePath", ...): Reads in base and quality information. Currently delegates to readFastaQual, above, but will do more after RochePath supports more file types.
readBaseQualitysignature(dirPath = "RochePath", ...)：读取碱基和质量信息。目前代表readFastaQual以上，但会做后RochePath支持更多的文件类型。
read454 signature(dirPath = "RochePath", ...): Pass
read454signature(dirPath = "RochePath", ...)：通过
readPath signature(object = "RochePath"): return the
readPathsignature(object = "RochePath")：返回
runNames signature(object = "RochePath"): return the
runNamessignature(object = "RochePath")：返回
RocheSet signature(path = "RochePath"): create a
RocheSetsignature(path = "RochePath")：创建一个
Additional methods include:
其他方法包括：
show signature(object = "RochePath"): Briefly
显示signature(object = "RochePath")：简要
detail signature(x = "RochePath"): Provide additional detail on the Roche path. All file paths are presented
详细signature(x = "RochePath")：罗氏路径提供更多细节。所有的文件路径
作者（S）----------Author(s)----------
Michael Lawrence <mflawrence@fhcrc.org>
参见----------See Also----------
ExperimentPath.
ExperimentPath。
举例----------Examples----------
showClass("RochePath")
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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 14:07:02
