AVASet(R453Plus1Toolbox)
AVASet()所属R语言包：R453Plus1Toolbox
Creating an AVASet
创建1 AVASet
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function imports a project of Roche's Amplicon Variant Analyzer Software. It stores all information into an extended version of the Biobase eSet.
此功能进口罗氏扩增变异分析仪软件的项目。它所有的信息存储到的BIOBASE ESET的扩展版本。
用法----------Usage----------
AVASet(dirname)
参数----------Arguments----------
参数：dirname
The path of the project data (i.e. a directory that contains the files and subdirectories "Amplicons/ProjectDef/ampliconsProject.txt", "Amplicons/Results/Variants/currentVariantDefs.txt", "Amplicons/Results/Variants", "Amplicons/Results/Align").
项目数据的路径（即目录，其中包含的文件和子目录“扩增/ ProjectDef / ampliconsProject.txt”，“扩增/ /变异/ currentVariantDefs.txt”，“扩增/结果/变种”，“ ;扩增/ /对齐“）。
Details
详情----------Details----------
An AVASet object consists of three slots to store data about <br> 1. variants <br>
AVASet对象包括三个插槽，存储数据有关参考1。变种参考
variantForwCount/variantRevCount: Data frames that contain the number of reads with the respective variant in forward/reverse
variantForwCount / variantRevCount：数据框包含的数量在正向/反向读取各自的变种
totalForwCount/totalRevCount: Data frames that contain the total coverage for every variant location in forward/reverse
totalForwCount / totalRevCount：数据框包含在前进的每一个变种位置的全覆盖/反转
referenceSeq: Gives the identifier of the reference sequence.
referenceSeq：提供参考序列标识符。
variantBase/referenceBases: The bases changed in each variant.
variantBase / referenceBases：在每个变种改变的基础。
start/end: The position of the variant on the reference sequence.
开始/结束：参考序列变异的位置。
canonicalPattern/name: Short identifiers of a variant including the position and the bases changed.
canonicalPattern /名称：改变一个变种的短标识符，包括位置和碱基。
2. amplicons <br>
2。扩增参考
forwCount/revCount: Data frames that contain the number of reads for every amplicon and each sample in
forwCount / revCount：读取数据框包含的数量为每扩增和每个样品
primer1,primer2: The primer sequences for every amplicon.
primer1，primer2：每扩增引物序列。
referenceSeqID: The identifier of the reference sequence.
referenceSeqID：参考序列标识符。
targetStart/targetEnd: The coordinates of the target region.
targetStart / targetEnd：目标区域的坐标。
3. reference sequences <br>
3。参考序列参考
The structure of the variant and amplicon data is derived from the Biobase eSet and thus separated into assayData, phenoData and featureData. All information about the reference sequences is stored into an object of class AlignedRead.
来自BIOBASE ESET结构变异和扩增数据，从而分离，到assayData，phenoData和featureData。有关的参考序列的所有信息存储到一个对象类AlignedRead。
The phenoData of the variants lists the sample-IDs and name, annotation and group of the read data for all samples. If available, the pico titer plate(s) (PTP) or MID(s) of each sample are shown as well.
变种phenoData列出了样品ID和名称，注释和所有样品的读取数据组。如果可以，滴度板的微型（S）（PTP）或MID（S）每个样品以及。
值----------Value----------
An instance of the AVASet class.
的AVASet类的实例。
作者（S）----------Author(s)----------
Christoph Bartenhagen
参见----------See Also----------
MapperSet-class, alignShortReads
MapperSet-class，alignShortReads
举例----------Examples----------
# load an AVA dataset containing 6 samples, 4 amplicons and 259 variants[加载AVA的数据集，其中包含6个样品，4扩增和259变种]
data(avaSetExample)
avaSetExample
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。
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 11:47:38
