assemble.data(SIM)
assemble.data()所属R语言包：SIM
Assemble the data to run the integrated analysis
组装的数据，运行综合分析
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Assembles the dependent and independent data and annotation of the both data sets.
组装依赖和独立的两个数据集的数据和注解。
用法----------Usage----------
assemble.data(dep.data,
indep.data,
dep.id = "ID",
dep.chr = "CHROMOSOME",
dep.pos = "STARTPOS",
dep.ann = NULL,
dep.symb,
indep.id = "ID",
indep.chr = "CHROMOSOME",
indep.pos = "STARTPOS",
indep.ann = NULL,
indep.symb,
overwrite = FALSE,
run.name = "analysis_results")
参数----------Arguments----------
参数：dep.data
The dependent data (data.frame), along with annotations. Each row should correspond to one feature. The following columns are expected to exist, and the column names should be inserted in the function. dep.id: A unique identifier. dep.chr: The number of the chromosome (1,2, ..., 22, X, Y). dep.pos: The base pair position, relative to the chromosome. dep.symb: Gene symbol (optional). dep.ann: Annotation can be multiple columns.
相关数据（data.frame），随着注释。每行对应一个功能。预计存在以下几列，列名应在插入功能。 dep.id：一个唯一的标识符。 dep.chr：（1,2，...，22日的X，Y）的染色体数目。 dep.pos：碱基对的位置，相对染色体。 dep.symb：基因符号（可选）。 dep.ann：注解可以多列。
参数：indep.data
data.frame The independent data, along with annotations. Each row should correspond to one feature. The following columns are expected to exist, and the column names should be inserted in the function. indep.id: A unique identifier. indep.chr: The number of the chromosome (1,2, ..., 22, X, Y). indep.pos: The base pair position, relative to the chromosome. indep.symb: Gene symbol (optional). indep.ann: Annotation can be multiple columns.
data.frame独立的数据，连同注释。每行对应一个功能。预计存在以下几列，列名应在插入功能。 indep.id：一个唯一的标识符。 indep.chr：（1,2，...，22日的X，Y）的染色体数目。 indep.pos：碱基对的位置，相对染色体。 indep.symb：基因符号（可选）。 indep.ann：注解可以多列。
参数：dep.ann
vector with either the names of the columns or the column numbers in the dependent data that contain the annotation.
vector的名字列或列数中包含注释的相关数据。
参数：indep.ann
vector with either the names of the columns or the column numbers in the independent data that contain the annotation.
vector列的名称或包含注释的独立的数据的列数。
参数：dep.id
vector with the column name in the dependent data that contains the ID. Will be used in the sim.plot.zscore.heatmap function. Empty ID's will be substituted by NA.
vector中的相关数据，包含ID的列名。将用于在sim.plot.zscore.heatmap功能。 NA空标识的将被替换。
参数：dep.chr
vector with column name in the dependent data that contains the chromosome numbers.
vector列名称中包含的染色体数目的相关数据。
参数：dep.pos
vector with the column name in the dependent data that contains the position on the chromosome in bases.
vector在包含在碱基染色体上的位置相关的数据的列名。
参数：dep.symb
Optional, either missing or a single vector with the column name in the dependent data that contains the symbols. Will be used in sim.plot.zscore.heatmap as label.
可选的，中的相关数据，其中包含符号的列名丢失或一个单一的向量。将用于在sim.plot.zscore.heatmap标签。
参数：indep.id
vector with the column name in the independent data that contains the ID. Will be used in the sim.plot.zscore.heatmap function. Empty ID's will be substituted by NA.
vector中包含独立的ID数据的列名。将用于在sim.plot.zscore.heatmap功能。 NA空标识的将被替换。
参数：indep.chr
vector with the column name in the independent data that contains the chromosome numbers.
vector独立的数据中包含的染色体数目的列名。
参数：indep.pos
vector with the column name in the independent data that contains the position on the chromosome in bases.
vector在包含在碱基染色体上的位置无关的数据的列名。
参数：indep.symb
Optional, either missing or a vector with the column name in the dependent data that contains the Symbols. Will be used in sim.plot.zscore.heatmap as label.
可选，丢失或与列名的相关数据，其中包含符号向量。将用于在sim.plot.zscore.heatmap标签。
参数：overwrite
logical, indicate when a run.name is already present, the results can be overwritten.
logical，run.name已经存在，其结果可能是覆盖。
参数：run.name
Name of the analysis. The results will be stored in a folder with this name in the current working directory (use getwd() to print the current working directory). If the missing, the default folder "analysis_results" will be generated.
分析名称。结果将被储存在一个具有此名称在当前工作目录的文件夹（使用getwd()打印当前工作目录）。如果缺少，默认的文件夹"analysis_results"将产生。
Details
详情----------Details----------
Based on the chromosome and probe position an absolute position is calculated according to chromosome number * 1e9 + probe position. Chromosome column is converted to factor and releveled according to the levels of the chrom.table, so the only levels allowed are c(1:22, "X", "Y"). Currently only human genome support without mitochondrial DNA.
基于染色体和探针位置绝对位置计算根据chromosome number * 1e9 + probe position。 ，染色体列转换到factor并releveled根据的chrom.table水平，因此，只允许水平c(1:22, "X", "Y")。目前，只有无线粒体DNA的人类基因组的支持。
值----------Value----------
No values are returned. Instead, the datasets and annotation columns are stored in separate files in the data folder in the directory specified in run.name. If assemble.data has run succesfully, the integrated.analysis function can be performed.
没有返回值。相反，数据集和注释列单独的文件存储在在data在run.name指定的目录中的文件夹中。如果assemble.data已成功地运行中，integrated.analysis功能可以执行。
作者（S）----------Author(s)----------
Marten Boetzer, Melle Sieswerda, Renee X. de Menezes <a href="mailto:R.X.Menezes@lumc.nl">R.X.Menezes@lumc.nl</a>
参见----------See Also----------
SIM, integrated.analysis
SIM卡，integrated.analysis
举例----------Examples----------
#load the datasets and the samples to run the integrated analysis[加载的数据集和样品运行综合分析]
data(expr.data)
data(acgh.data)
data(samples)
#assemble the data[装配数据]
assemble.data(dep.data = acgh.data,
indep.data = expr.data,
dep.id="ID",
dep.chr = "CHROMOSOME",
dep.pos = "STARTPOS",
dep.ann = colnames(acgh.data)[1:4],
dep.symb="Symbol",
indep.id="ID",
indep.chr = "CHROMOSOME",
indep.pos = "STARTPOS",
indep.ann = colnames(expr.data)[1:4],
indep.symb="Symbol",
overwrite = TRUE,
run.name = "chr8q")
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 14:22:56
