SolexaSet-class(ShortRead)
SolexaSet-class()所属R语言包：ShortRead
"SolexaSet" coordinating Solexa output locations with sample annotations
“SolexaSet”协调公司Solexa样品注释输出位置
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This class coordinates the file hierarchy produced by the Solexa "pipeline" with annotation data contained in an AnnotatedDataFrame (defined in the Biobase package).
这个类负责协调公司Solexa“管道”的注释中包含的数据所产生的文件层次结构AnnotatedDataFrame（Biobase包中定义）。
类的对象----------Objects from the Class----------
Objects can be created from the constructor:
可以从构造函数创建对象：
SolexaSet(path, ...).
SolexaSet(path, ...)。
path A character(1) vector giving the fully-qualified path to the root of the directory hierarchy associated with each Solexa flow cell, or an object of class SolexaPath (see
路径Acharacter(1)向量与每个公司Solexa流单元相关的目录层次结构的根，或一个类的对象的完全限定路径SolexaPath（见
... Additional arguments, especially laneDescription, an AnnotatedDataFrame describing the content of each of the 8 lanes in the Solexa flow
...额外的参数，尤其是laneDescription，AnnotatedDataFrame8车道的内容描述在公司Solexa流
插槽----------Slots----------
SolexaSet has the following slots:
SolexaSet有以下插槽：
solexaPath: Object of class "SolexaPath".
solexaPath类"SolexaPath"的对象。
laneDescription: Object of class "AnnotatedDataFrame", containing information about the
laneDescription类"AnnotatedDataFrame"，其中包含有关信息：对象
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----------
solexaPath signature(object = "SolexaSet"): Return the directory paths present when this object was created as a
solexaPathsignature(object = "SolexaSet")：返回路径中时，这个对象作为创建目录
laneNames signature(object = "SolexaSet"): Return the names of each lane in the flow cell, currently names are simply
laneNamessignature(object = "SolexaSet")：返回流中的单元的每个车道的名称，目前名是根本
show signature(object = "SolexaSet"): Briefly summarize the experiment path and lane description of the Solexa
显示signature(object = "SolexaSet")：简要总结实验路径的公司Solexa车道描述
detail signature(x = "SolexaSet"): Provide additional detail on the Solexa set, including the content of solexaPath and the pData and varMetadata of
详细signature(x = "SolexaSet")：公司Solexa集提供更多的细节，包括的内容solexaPath和pData和varMetadata
Methods transforming SolexaSet objects include:
转化SolexaSet对象的方法包括：
signature(dirPath = "SolexaSet", pattern = ".*_export.txt", run, ..., filter=srFilter()):
signature(dirPath = "SolexaSet", pattern = ".*_export.txt", run, ..., filter=srFilter())：
Use analysisPath(solexaPath(dirPath))[run] as the directory path(s) 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 specific chromosomes,
使用analysisPath(solexaPath(dirPath))[run]目录路径（S）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选择的特定染色体的对象，
作者（S）----------Author(s)----------
Martin Morgan
举例----------Examples----------
showClass("SolexaSet")
showMethods(class="SolexaSet", where=getNamespace("ShortRead"))
## construct a SolexaSet[＃1 SolexaSet建设]
sf <- system.file("extdata", package="ShortRead")
df <- data.frame(Sample=c("Sample 1", "Sample 2", "Sample 3", "Sample
4", "Center-wide control", "Sample 6", "Sample
7", "Sample 8"),
Genome=c(rep("hg18", 4), "phi_plus_SNPs.txt",
rep("hg18", 3)))
dfMeta <- data.frame(labelDescription=c("Type of sample",
"Alignment genome"))
adf <- new("AnnotatedDataFrame", data=df, varMetadata=dfMeta)
SolexaSet(sf, adf)
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。
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发表于 2012-2-26 14:09:02
