SolexaPath-class(ShortRead)
SolexaPath-class()所属R语言包：ShortRead
"SolexaPath" class representing a standard output file hierarchy
“SolexaPath”类代表标准输出文件层次结构
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Solexa produces a hierarchy of output files. The content of the hierarchy varies depending on analysis options. This class represents a standard class hierarchy, constructed by searching a file hierarchy for appropriately named directories.
公司Solexa产生的输出文件的层次结构。根据分析选项不同层次的内容。这个类代表一个标准的类层次结构，通过寻找适当命名的目录文件层次结构构造。
类的对象----------Objects from the Class----------
Objects from the class are created by calls to the constructor:
从类创建对象的构造函数的调用：
SolexaPath(experimentPath, dataPath=.solexaPath(experimentPath, "Data"), scanPath=.solexaPath(dataPath, "GoldCrest"), imageAnalysisPath=.solexaPath(dataPath, "^(C|IPAR)"), baseCallPath=.solexaPath(imageAnalysisPath, "^Bustard"), analysisPath=.solexaPath(baseCallPath, "^GERALD"), ..., verbose=FALSE)
SolexaPath(experimentPath, dataPath=.solexaPath(experimentPath, "Data"), scanPath=.solexaPath(dataPath, "GoldCrest"), imageAnalysisPath=.solexaPath(dataPath, "^(C|IPAR)"), baseCallPath=.solexaPath(imageAnalysisPath, "^Bustard"), analysisPath=.solexaPath(baseCallPath, "^GERALD"), ..., verbose=FALSE)
experimentPath character(1) object pointing to the top-level directory of a Solexa run, e.g., /home/solexa/user/080220_HWI-EAS88_0004. This is the only
experimentPathcharacter(1)对象指向一个公司Solexa运行的顶层目录，例如，/home/solexa/user/080220_HWI-EAS88_0004。这是唯一的
dataPath (optional) Solexa "Data" folder .
数据路径（可选）公司Solexa“数据”文件夹。
scanPath (optional) Solexa GoldCrest image scan path.
scanPath（可选）公司Solexa GoldCrest图像扫描路径。
imageAnalysisPath (optional) Firecrest image analysis path.
imageAnalysisPath（可选）Firecrest的图像分析路径。
baseCallPath (optional) Bustard base call path.
baseCallPath（可选）鸨碱基呼叫路径。
analysisPath (optional) Gerald analysis pipeline path.
analysisPath（可选）杰拉尔德分析管道路径。
... Additional arguments, unused by currently implemented
...未使用的，由目前执行的额外的参数
verbose=FALSE (optional) logical vector which, when
VERBOSE = FALSE（可选），当逻辑向量
All paths must be fully-specified.
所有的路径，必须充分规定。
插槽----------Slots----------
SolexaPath has the following slots, containing either a fully specified path to the corresponding directory (described above) or NA if no appropriate directory was discovered.
SolexaPath有以下插槽，包含一个完全指定的路径到相应的目录（如上所述）或NA如果没有相应的目录中被发现。
basePath See experimentPath, above.
basePath见experimentPath以上。
dataPath See above.
dataPath见上面。
scanPath See above.
scanPath见上面。
imageAnalysisPath See above.
imageAnalysisPath见上面。
baseCallPath See above.
baseCallPath见上面。
analysisPath See above.
analysisPath见上面。
延伸----------Extends----------
Class ".Solexa", directly. Class ".ShortReadBase", by class ".Solexa", distance 2.
类".Solexa"，直接。类".ShortReadBase"“类”。公司Solexa“，距离为2。
方法----------Methods----------
Transforming methods include:
转化的方法包括：
signature(dirPath = "SolexaPath", pattern=character(0), run, ...):
signature(dirPath = "SolexaPath", pattern=character(0), run, ...)：
Use imageAnalysisPath(sp)[run] as the directory path(s) and pattern=character(0) as the pattern for discovering Solexa intensity files. See readIntensities,character-method for additional
使用imageAnalysisPath(sp)[run]目录路径（S）和pattern=character(0)用于发现公司Solexa强度文件的模式。看到readIntensities,character-method额外
signature(dirPath = "SolexaPath", pattern=character(0), run, ...):
signature(dirPath = "SolexaPath", pattern=character(0), run, ...)：
Use baseCallPath(dirPath)[run] as the directory path(s) and pattern=character(0) as the pattern for discovering Solexa "prb" files, returning a SFastqQuality object containing the maximum qualities found for each base of each cycle.
使用baseCallPath(dirPath)[run]目录路径（S）和pattern=character(0)发现公司Solexa“PRB”文件，返回一个SFastqQuality对象包含每个每个周期的基础上发现的最大素质格局。
The ... argument may include the named argument as. This influences the return value, as explained on the readPrb,character-method page.
...参数可能包括命名参数as。这影响的返回值，如readPrb,character-method页解释。
signature(dirPath, pattern = character(0), ..., nrec=-1L, skip=0L):
signature(dirPath, pattern = character(0), ..., nrec=-1L, skip=0L)：
Use analysisPath(dirPath)[run] as the directory path(s) for discovering fasta-formatted files, returning a ShortRead object. The default method reads
使用analysisPath(dirPath)[run]发现FASTA格式的文件，返回ShortRead对象的目录路径（S）。默认的方法读取
signature(dirPath = "SolexaPath", pattern = ".*_sequence.txt", run, ..., qualityType="SFastqQuality"):
signature(dirPath = "SolexaPath", pattern = ".*_sequence.txt", run, ..., qualityType="SFastqQuality")：
Use analysisPath(dirPath)[run] as the directory path(s) and pattern=".*_sequence.txt" as the pattern for discovering fastq-formatted files, returning a ShortReadQ object. The default method reads all sequence files into a
使用analysisPath(dirPath)[run]目录路径（S）和pattern=".*_sequence.txt"作为发现fastq格式的文件，返回ShortReadQ对象的模式。默认的方法都变成了读取序列文件
signature(dirPath = "SolexaPath", seqPattern = ".*_seq.txt", prbPattern = "s_[1-8]_prb.txt", run, ...):
signature(dirPath = "SolexaPath", seqPattern = ".*_seq.txt", prbPattern = "s_[1-8]_prb.txt", run, ...)：
Use baseCallPath(dirPath)[run] as the directory path(s) and seqPattern=".*_seq.txt" as the pattern for discovering base calls and prbPattern=".*_prb.txt" as the pattern for discovering quality scores. Note that the default method reads all base call and quality score files into a single object;
使用baseCallPath(dirPath)[run]目录路径（S）和seqPattern=".*_seq.txt"发现碱基检测和模式prbPattern=".*_prb.txt"如发现质量分数的格局。请注意，默认的方法读取所有基本通话和质量得分文件到一个单一的对象;
signature(directory="SolexaPath", pattern=".*_qseq.txt.*", run, ...., filtered=FALSE):
signature(directory="SolexaPath", pattern=".*_qseq.txt.*", run, ...., filtered=FALSE)：
Use analysisPath(dirPath)[run] as the directory path and pattern=".*_qseq.txt.*" as the pattern for discovering read and quality scores in Solexa 'qseq' files. Data from all files are read into a single object; often one will want to specify a pattern for each lane. Details are as for
使用analysisPath(dirPath)[run]目录路径和pattern=".*_qseq.txt.*"公司Solexa“qseq”文件中发现只读和质量得分模式。所有文件中的数据读入一个单一的对象，常常会想为每个通道指定一个模式。详情为
signature(dirPath = "SolexaPath", pattern = ".*_export.txt.*", run, ..., filter=srFilter()):
signature(dirPath = "SolexaPath", pattern = ".*_export.txt.*", run, ..., filter=srFilter())：
Use analysisPath(dirPath)[run] as the directory path and pattern=".*_export.txt" as the pattern for discovering Eland-aligned reads in the Solexa 'export' file format. Note that the default method reads all aligned read files into a single object; often one will want to specify a pattern for each lane. Use an object of SRFilter to select
使用analysisPath(dirPath)[run]目录路径和pattern=".*_export.txt"发现伊兰对齐模式，在公司Solexa“出口”的文件格式读取。需要注意的是默认的方法读取所有对齐的读文件到一个单一的对象，常常会想为每个通道指定一个模式。使用SRFilter选择的对象
signature(dirPath="SolexaPath", pattern="character(0)", run, ...):
signature(dirPath="SolexaPath", pattern="character(0)", run, ...)：
Use analysisPath(dirPath)[run] as the directory path(s) and pattern=".*_export.txt" as the pattern for discovering Solexa export-formatted fileds, returning a SolexaExportQA object summarizing quality assessment. If Rmpi or parallel has been initiated, quality assessment calculations are distributed across available
使用analysisPath(dirPath)[run]目录路径（S）和pattern=".*_export.txt"发现公司Solexaexport格式化个行业，返回SolexaExportQA对象总结质量评估的模式。如果Rmpi或parallel已经启动，质量评估计算分布在可用
signature(x, ..., dest=tempfile(), type="pdf"): Use qa(x, ...) to generate quality assessment measures, and use these to generate a quality assessment report at location dest of type type (e.g., "pdf").
signature(x, ..., dest=tempfile(), type="pdf")：使用qa(x, ...)生成质量评估措施，并使用这些位置产生的质量评估报告dest型type（如PDF）。
SolexaSet signature(path = "SolexaPath"): create a
SolexaSetsignature(path = "SolexaPath")：创建一个
Additional methods include:
其他方法包括：
show signature(object = "SolexaPath"): briefly summarize the file paths of object. The experimentPath is given in full; the remaining paths are
显示signature(object = "SolexaPath")：简要总结文件路径object。 experimentPath给予充分;其余的路径是
detail signature(x = "SolexaPath"): summarize file paths of x. All file paths are presented in
详细signature(x = "SolexaPath")：总结x的文件路径。所有文件路径
作者（S）----------Author(s)----------
Martin Morgan
举例----------Examples----------
showClass("SolexaPath")
showMethods(class="SolexaPath", where=getNamespace("ShortRead"))
sf <- system.file("extdata", package="ShortRead")
sp <- SolexaPath(sf)
sp
readFastq(sp, pattern="s_1_sequence.txt")
## Not run: [＃无法运行：]
nfiles <- length(list.files(analysisPath(sp), "s_[1-8]_export.txt"))
library(Rmpi)
mpi.spawn.Rslaves(nslaves=nfiles)
report(qa(sp))
## End(Not run)[＃结束（不运行）]
## Not run: [＃无法运行：]
nfiles <- length(list.files(analysisPath(sp), "s_[1-8]_export.txt"))
library(parallel)
options(srapply_fapply="parallel")
report(qa(sp))
## End(Not run)[＃结束（不运行）]
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注：
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发表于 2012-2-26 14:08:47
