read.ilmn(limma)
read.ilmn()所属R语言包：limma
Read Illumina Expression Data
阅读Illumina的表达数据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Read Illumina summary probe profile files and summary control probe profile files
阅读Illumina的总结探针profile文件和总结控制探针设定档
用法----------Usage----------
read.ilmn(files=NULL, ctrlfiles=NULL, path=NULL, ctrlpath=NULL,
probeid="Probe", annotation=c("TargetID", "SYMBOL"), expr="AVG_Signal", other.columns="Detection",
sep="\t", quote="\"", verbose=TRUE, ...)
参数----------Arguments----------
参数：files
character vector giving the names of the summary probe profile files.
特征向量摘要探针profile文件的名称。
参数：ctrlfiles
character vector giving the names of the summary control probe profile files.
特征向量摘要控制探针profile文件的名称。
参数：path
character string giving the directory containing the summary probe profile files. The default is the current working directory.
字符串给摘要探针profile文件包含目录。默认为当前工作目录。
参数：ctrlpath
character string giving the directory containing the summary control probe profile files. The default is the current working directory.
字符串给予含摘要控制探针设定档目录。默认为当前工作目录。
参数：probeid
character string giving the name of the probe identifier column.
字符串探针标识符列的名称。
参数：annotation
character vector giving possible names of the annotation column. It could be called "TargetID" or "SYMBOL" depending on which version of BeadStudio is used.
字符向量注释列可能的名字。它可以被称为“目标ID”或“符号”，取决于使用其中BeadStudio版本。
参数：expr
character string giving the keyword in the names of the expression intensity columns.
字符串表达强度列的名称中的关键字。
参数：other.columns
character vector giving the keywords in the names of extra columns required, such as "Detection", "Avg_NBEADS", "BEAD_STDEV" etc. Each keyword corresponds to one type of columns. The detection p value columns will be read in by default.
特征向量给需要额外的列，如“检测”，“Avg_NBEADS”，“BEAD_STDEV”等每个关键字对应一个列的类型，名称中的关键字。检测P值列将在默认情况下被读取。
参数：sep
the field separator character.
字段分隔符。
参数：quote
character string of characters to be treated as quote marks.
被视为引号字符字符串。
参数：verbose
logical, TRUE to report names of profile files being read.
逻辑，TRUE报告正在读取的设定档名称。
参数：...
any other parameters are passed on to read.columns.
任何其他参数被传递到read.columns。
Details
详情----------Details----------
Illumina BeadStudio ouputs probe intensities (regular probe intensities) and control probe intensities to summary probe profile files (containing regular probes) and summary control probe profile files, respectively. If both files and ctrlfiles are not NULL, this function will combine the data read from the two file types and save them to an EListRaw-class object. If one of them is NULL, then only the required data are read in.
Illumina的BeadStudio ouputs探针强度（常规探针强度）和控制探针强度摘要探针设定档（含定期探针）和总结控制探针设定档，分别为。如果双方files和ctrlfiles非NULL，此功能将结合从两种类型的文件中读取数据，并将它们保存到一个EListRaw-class对象。如果其中一个是NULL，那么只有所需的数据读入。
Probe types are indicated in the Status column of genes, a component of the returned EListRaw-class object. There are totally seven types of control probes including negative, biotin, labeling, cy3_hyb, housekeeping, high_stringency_hyb or low_stringency_hyb. Regular probes have the probe type regular. The Status column will not be created if ctrlfiles is NULL.
探针类型Statusgenes列表示，返回EListRaw-class对象的一个组成部分。总共有七个控制探针类型，包括negative，biotin，labeling，cy3_hyb，housekeeping，high_stringency_hyb或low_stringency_hyb 。定期探针探针类型regular。不会创建Status是ctrlfilesNULL列。
To read in columns other than probeid, annotation and expr, users needs to specify keywords in other.columns. One keyword corresponds to one type of columns. Examples of keywords are "Detection", "Avg_NBEADS", "BEAD_STDEV" etc.
要阅读其他列比probeid，annotation和expr，用户需要指定other.columns的关键字。一个关键字对应一个列的类型。关键字的例子是“检测”，“Avg_NBEADS”，“BEAD_STDEV”等。
值----------Value----------
An EListRaw-class object with the following components:
EListRaw-class对象有下列组件：
参数：E
numeric matrix of raw intensities.
数字矩阵的原始强度。
参数：genes
data.frame of probe annotation.
数据框标注的探针。
参数：targets
data.frame of sample information.
数据框的样本资料。
参数：other
list of other column data.
其他列的数据列表。
作者（S）----------Author(s)----------
Wei Shi and Gordon K Smyth
参见----------See Also----------
read.ilmn.targets reads in Illumina expression data using the file information extracted from a target data frame which is often created by the readTargets function.
read.ilmn.targetsIllumina的表达，使用的文件从readTargets函数通常是由创建目标数据框中提取的信息数据读取。
neqc performs normexp by control background correction, log transformation and quantile between-array normalization for Illumina expression data.
neqc执行normexp通过控制背景校正，记录改造和Illumina的表达数据的位数之间的阵列标准化。
normexp.fit.control estimates the parameters of the normal+exponential convolution model with the help of negative control probes.
normexp.fit.control估计与阴性对照探针的帮助下，指数正常+卷积模型的参数。
propexpr estimates the proportion of expressed probes in a microarray.
propexpr估计在一个芯片中表示探针的比例。
举例----------Examples----------
## Not run: [＃无法运行：]
x <- read.ilmn(files="sample probe profile.txt",ctrlfiles="control probe profile.txt")
## End(Not run)[＃结束（不运行）]
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 2012-2-25 23:24:25
