MapperSet-class(R453Plus1Toolbox)
MapperSet-class()所属R语言包：R453Plus1Toolbox
Class to Contain GS Reference Mapper Output
一类含有GS参考映射输出
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Container to store data imported from a project of Roche's GS Reference Mapper Software. It stores all information into a Biobase ExpressionSet.
从罗氏公司的GS参考Mapper软件项目进口的数据存储容器。它所有的信息存储到一个BIOBASE ExpressionSet。
类的对象----------Objects from the Class----------
Objects can be created by calls of the form MapperSet(filename). While filename is a vector containing all sample directories (i.e. directories that contain the files "mapping/454HCDiffs.txt" and "mapping/454NewblerMetrics.txt").
创建对象可以通过检测的形式MapperSet(filename)。虽然文件名是一个向量，所有样品目录（即包含文件“mapping/454HCDiffs.txt”和“mapping/454NewblerMetrics.txt”的目录）。
插槽----------Slots----------
assayData: Object of class AssayData. Contains the number of reads with the respective difference and the total coverage
assayData类AssayData的对象。包含读取次数与各自的差异和全覆盖
featureData: Object of class AnnotatedDataFrame. Contains information about the type, location and reference of each
featureData类AnnotatedDataFrame的对象。包含有关信息的类型，位置和每个参考
phenoData: Object of class AnnotatedDataFrame. By default, the phenoData contains the accession number of every sample.
phenoData类AnnotatedDataFrame的对象。默认情况下，phenoData包含每个样品加入。
variantFilterPerc: Object of class numeric. Contains a threshold to display only those variants, whose coverage (in percent) in forward and reverse direction in at least one sample is higher than this filter value. See
variantFilterPerc类numeric的对象。包含一个阈值，以显示只有那些变种，其覆盖率（％）至少有一个样本是在正向和反向高于此过滤器的值。见
variantFilter: Object of class character. Contains a vector of variant names whose coverage (in percent) in forward and reverse direction in at least one sample is higher than the filter value(s) in
variantFilter类character的对象。包含一个矢量的覆盖率（％）至少有一个样本是在正向和反向高于过滤器值（S）的变种名称
dirs: Object of class character. Based on a directory given at instantiation of the object, it contains a vector of several
dirs类character的对象。基于对象的实例目录，它包含了几个向量
experimentData: Object of class MIAME. Contains details of the experiment.
experimentData类MIAME的对象。包含实验的细节。
annotation: Object of class character Label associated with the annotation package used in the experiment.
annotation类character在实验中使用的注释包标签的对象。
protocolData: Object of class AnnotatedDataFrame. Contains additional information about the samples.
protocolData类AnnotatedDataFrame的对象。包含有关样本的额外信息。
.__classVersion__: Object of class Versions. Remembers the R and R453Toolbox version numbers used to created the
.__classVersion__类Versions的对象。记得以创建使用R和R453Toolbox版本号
延伸----------Extends----------
Class eSet, directly. Class VersionedBiobase, by class "eSet", distance 2. Class Versioned, by class "eSet", distance 3.
类eSet，直接。类VersionedBiobase，“ESET”级，距离为2。类Versioned，“ESET”级，距离3。
方法----------Methods----------
setVariantFilter(object): Sets the filter to display only those variants, whose coverage (in percent) in forward and reverse
setVariantFilter（对象）：设置过滤器显示只有那些变种，在前进的覆盖率（％）和扭转
getVariantPercentages(object) Computes the coverage for every variant over all reads (forward and/or reverse) and for each
getVariantPercentages（对象），计算每超过所有读取的变种（正向和/或反向），并为每个覆盖
annotateVariants(object): Annotates given genomic variants. See annotateVariants for details.
annotateVariants（对象）：注基因变种。看到annotateVariants详情。
htmlReport(object): Exports all (filtered) variant data into a html report. See htmlReport for details
htmlReport（对象）：出口（过滤）Variant数据到一个HTML报告。 htmlReport详情
getReadStatus(object): Reads the file "454ReadStatus.txt" in the GSM project directory which contains information about the
getReadStatus（对象）：在GSM项目目录，其中包含有关信息读取文件“454ReadStatus.txt”
作者（S）----------Author(s)----------
Christoph Bartenhagen
参见----------See Also----------
AVASet, annotateVariants, htmlReport, setVariantFilter, getVariantPercentages
AVASet，annotateVariants，htmlReport，setVariantFilter，getVariantPercentages
举例----------Examples----------
# sum up class structure[总结班级结构]
showClass("MapperSet")
# load a GS Mapper dataset containing 3 samples and 111 variants[加载GS映射集包含3个样本和111变种]
data(mapperSetExample)
mapperSetExample
# show contents of assay, feature and pheno data[分析，功能和苯酚数据显示的内容]
assayData(mapperSetExample)
fData(mapperSetExample)
pData(mapperSetExample)
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 11:50:46
