qa(ShortRead)
qa()所属R语言包：ShortRead
Perform quality assessment on short reads
短期读取执行质量评估
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function is a common interface to quality assessment functions available in ShortRead. Results from this function may be displayed in brief, or integrated into reports using, e.g., report.
此功能是一种常见的接口质量评估功能，可在ShortRead。从这个函数的结果可以显示在短暂的，或集成到使用报告，例如，report。
用法----------Usage----------
qa(dirPath, ...)
## S4 method for signature 'character'
qa(dirPath, pattern=character(0),
type=c("SolexaExport", "SolexaRealign", "Bowtie", "MAQMap",
"MAQMapShort", "fastq", "BAM"),
...)
## S4 method for signature 'list'
qa(dirPath, ...)
参数----------Arguments----------
参数：dirPath
A character vector or other object (e.g., SolexaPath; see showMethods, below) locating the data for which quality assessment is to be performed. See help pages for defined methods (by evaluating the example code, below) for details of available methods.
一个特征向量或其他对象（例如，SolexaPath见showMethods，下面）定位数据进行质量评估。定义的方法可用方法的详细信息，通过评估下面的示例代码，请参阅帮助页。
参数：pattern
A character vector limiting the files in dirPath to be processed, as with list.files. Care should be taken to specify pattern to avoid reading unintended files.
限制文件的字符向量dirPath处理list.files的。应采取指定的模式，以避免意外的文件阅读。
参数：type
The type of file being parsed; must be a character vector of length 1, selected from one of the types enumerated in the parameter.
被解析的文件类型，必须是一个长度为1的特征向量选择，从参数中所列举的类型之一。
参数：...
Additional arguments used by methods.
方法使用额外的参数。
fapply, reduce:Influence how evaluation occurs when this function is run with the Rmpi or parallel packages; see srapply.
fapply，reduce：影响如何评价此功能时发生的Rmpi或parallel包运行;看到srapply。
Lpattern, Rpattern:A character vector or XString object to be matched to the left end of a sequence. If either Lpattern or Rpattern are provided, trimLRPatterns is invoked to produce a measure of adapter contamination. Mismatch rates are 0.1 on the left and 0.2 on the right, with a minimum overlap of 10 nt.
Lpattern，Rpattern：字符向量或XString对象的匹配序列的左端。如果任Lpattern或Rpattern是trimLRPatterns调用产生一个适配器污染的措施。错配率是0.1的左侧和右侧的0.2，最低10 NT重叠。
Details
详情----------Details----------
The following methods are defined, in addition to those on S4 formal classes documented elsewhere:
下面的方法定义，除了记录在其他地方的中S4中正规类：
Quality assessment is performed on all files in directory dirPath whose file name matches pattern. The type of analysis performed is based on the type argument. Use SolexaExport when all files matching pattern are Solexa _export.txt files. Use SolexaRealign for Solexa _realign.txt files. Use Bowtie for Bowtie files. Use MAQMapShort for MAQ map files produced by MAQ versions below 0.70 and MAQMap for more recent output. Use fastq for collections of fastq-format files. Use BAM for .bam files; see the param argument in readAligned for information on how to influence reads included in the qa summary. Quality assessment details vary depending on data source.
执行中的所有文件目录dirPath的文件名匹配pattern质量评估。 type参数类型进行分析的基础上。使用SolexaExport当所有匹配的文件pattern是公司Solexa_export.txt文件。使用SolexaRealign公司Solexa_realign.txt文件。使用Bowtie领结文件。使用MAQMapShort MAQmap由MAQ版本低于0.70MAQMap更近的输出产生的文件。使用fastq集合fastq格式的文件的。使用BAM.bam文件;看到param参数readAligned如何影响读取包含在QA摘要信息。质量评估的详细情况各不相同，取决于数据源。
dirPath is a list of objects, all of the same class and typically derived from ShortReadQ, on which quality assessment is performed. All elements of the list must have names, and these should be unique.
dirPath是一个对象的名单，所有在同一类的，通常从ShortReadQ，进行质量评估而得。列表中的所有元素都必须有名字，这应该是唯一的。
值----------Value----------
An object derived from class .QA. Values contained in this object are meant for use by report
来自一个对象类.QA。在此对象中的值意味着使用report
作者（S）----------Author(s)----------
Martin Morgan <mtmorgan@fhcrc.org>
参见----------See Also----------
.QA, SolexaExportQA MAQMapQA FastqQA BAMQA
.QA，SolexaExportQAMAQMapQAFastqQABAMQA
举例----------Examples----------
sp <- SolexaPath(system.file("extdata", package = "ShortRead"))
qa1 <- qa(sp)
fq <- file.path(analysisPath(sp), pattern="s_1_sequence.txt")
qa2 <- qa(readFastq(fq), basename(fq)) # name fastq files[名称fastq文件]
showMethods("qa", where=getNamespace("ShortRead"))
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。
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发表于 2012-2-26 14:05:00
