readBeadSummaryData(beadarray)
readBeadSummaryData()所属R语言包：beadarray
Read BeadStudio gene expression output
阅读BeadStudio基因表达输出
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function to read the output of Illumina's BeadStudio software into beadarray
函数读取到输出Illumina的BeadStudio软件beadarray
用法----------Usage----------
readBeadSummaryData(dataFile, qcFile=NULL, sampleSheet=NULL,
sep="\t", skip=8, ProbeID="ProbeID",
columns = list(exprs = "AVG_Signal", se.exprs="BEAD_STDERR",
nObservations = "Avg_NBEADS", Detection="Detection Pval"),
qc.sep="\t", qc.skip=8, controlID="ProbeID",
qc.columns = list(exprs="AVG_Signal", se.exprs="BEAD_STDERR",
nObservations="Avg_NBEADS", Detection="Detection Pval"),
illuminaAnnotation=NULL, dec=".", quote="", annoCols = c("TargetID", "PROBE_ID","SYMBOL"))
参数----------Arguments----------
参数：dataFile
character string specifying the name of the file containing the BeadStudio output for each probe on each array in an experiment (required). Ideally this should be the 'SampleProbeProfile' from BeadStudio.
字符串指定的包含在一个实验（必需）每个探针对每个阵列BeadStudio输出文件的名称。理想的情况下，这应该是SampleProbeProfile从BeadStudio的。
参数：qcFile
character string giving the name of the file containing the control probe intensities (optional). This file should be either the 'ControlProbeProfile' or 'ControlGeneProfile' from BeadStudio.
含有控制探针强度（可选）的文件名字符串。这个文件应该是要么“ControlProbeProfile或”ControlGeneProfile从BeadStudio的。
参数：sampleSheet
character string used to specify the file containing sample infomation (optional)
字符串，用于指定文件包含样品infomation（可选）
参数：sep
field separator character for the dataFile ("\t" for tab delimited or "," for comma separated)
场分隔符dataFile（"\t"为制表符分隔或","逗号分隔）
参数：skip
number of header lines to skip at the top of dataFile. Default value is 8.
标题行数跳过在dataFile顶部。默认值是8。
参数：ProbeID
character string of the column in dataFile that contains identifiers that can be used to uniquely identify each probe
dataFile，列的字符字符串包含标识符可以用来唯一标识每个探针
参数：columns
list defining the column headings in dataFile which correspond to the matrices stored in the assayData slot of the final ExpressionSetIllumina object
dataFile对应的矩阵存储assayData最后ExpressionSetIllumina对象插槽中的列标题列表定义
参数：qc.sep
field separator character for qcFile
字段分隔符qcFile
参数：qc.skip
number of header lines to skip at the top of qcFile
标题行数，跳过在的qcFile顶部
参数：controlID
character string specifying the column in qcFile that contains the identifiers that uniquely identify each control probe
qcFile，指定列的字符串包含标识符唯一标识每个监控探针
参数：qc.columns
list defining the column headings in qcFile which correspond to the matrices stored in the QCInfo slot of the final ExpressionSetIllumina object
qcFile对应的矩阵存储QCInfo最后ExpressionSetIllumina对象插槽中的列标题列表定义
参数：illuminaAnnotation
character string specifying the name of the annotation package (only available for certain expression arrays at present)
字符串指定的注解包（目前仅适用于某些表达阵列）的名称
参数：dec
the character used in the dataFile and qcFile for decimal points
使用的字符dataFile和qcFile小数点
参数：quote
the set of quoting characters (disabled by default)
引用字符集（默认禁用）
参数：annoCols
additional columns containing annotation to be read from the file
额外的列包含注释，从文件中读取
Details
详情----------Details----------
This function can be used to read gene expression data exported from versions 1,2 and 3 of the Illumina BeadStudio application. The format of the BeadStudio output will depend on the version number. For example, the file may be comma or tab separated of have header information at the top of the file. The parameters sep and skip can be used to adapt the function as required (i.e. skip=7 is appropriate for data from earlier version of BeadStudio, and skip=0 is required if header information hasn't been exported.
这个功能可以被用来读取基因的表达，从版本1,2和3 Illumina公司BeadStudio应用导出的数据。的BeadStudio输出的格式将取决于版本号。例如，该文件可能是逗号或制表符分隔在文件的顶部有头信息。参数sep和skip可以用来适应的功能要求（即跳过= 7是适用于数据从早期版本的BeadStudio，跳过= 0头信息没有出口。
The format of the BeadStudio file is assumed to have one row for each probe sequence in the experiment and a set number of columns for each array. The columns which are exported for each array are chosen by the user when running BeadStudio. At a minimum, columns for average intensity standard error, the number of beads and detection scores should be exported, along with a column which contains a unique identifier for each bead type (usually named "ProbeID").
假设有一排每个探针序列的实验，并为每个阵列的列数的BeadStudio文件的格式。为每个阵列出口列由用户选择在运行BeadStudio时。在最低限度，平均强度标准错误的列，数珠和检测分数应出口，随着一列，其中包含了每个珠型（通常命名为“ProbeID”）的唯一标识符。
It is assumed that the average bead intensities for each array appear in columns with headings of the form 'AVG\_Signal-ARRAY1', 'AVG\_Signal-ARRAY2',...,'AVG\_Signal-ARRAYN' for the N arrays found in the file. All other column headings are matched in the same way using the character strings specified in the columns argument.
据推测，平均每个阵列珠强度出现在列标题的形式AVG \ _Signal ARRAY1“，”平均\ _Signal array2的，...，AVG \ _Signal-ARRAYN为N阵列在文件中找到。所有其他的列标题是在相同的方式使用字符columns参数指定的字符串的匹配。
NOTE: With version 2 of BeadStudio it is possible to export annotation and sequence information along with the intensities. We \_don't\_ recommend exporting this information, as special characters found in the annotation columns can cause problems when reading in the data. This annotation information can be retrieved later on from other Bioconductor packages.
注：与2 BeadStudio版本，它是可能的强度随着出口的注释和序列信息。我们\ _dont \ _建议将此信息导出，注释列中发现的特殊字符在读取数据时，可能会导致问题。此批注的信息可以从其他Bioconductor包以后检索。
The default object created by readBeadSummaryData is an ExpressionSetIllumina object.
默认的对象由readBeadSummaryData创建，是一个ExpressionSetIllumina对象。
If the control intensities have been exported from BeadStudio ('ControlProbeProfile') this may be read into beadarray as well. The qc.skip, qc.sep and qc.columns parameters can be used to adjust for the contents of the file. If the 'ControlGeneProfile' is exported, you will need to set controlID="TargetID".
如果控制强度已从BeadStudio出口（“ControlProbeProfile）可以读入beadarray以及。 qc.skip，qc.sep和qc.columns参数，可以用来调整文件的内容。如果出口“ControlGeneProfile”，您将需要设置controlID="TargetID"。
Sample sheet information can also be used. This is a file format used by Illumina to specify which sample has been hybridised to each array in the experiment.
也可用于样品表信息。这是一种文件格式，由Illumina公司用于指定样品已hybridised在实验中给每个阵列。
Note that if the probe identifiers are non-unique, the duplicated rows are removed. This may occur if the 'SampleGeneProfile' is exported from BeadStudio and/or ProbeID="TargetID" is specified (the "ProbeID" column has a unique identifier in the 'SampleProbeProfile', whereas the "TargetID" may not, as multiple beads can target the same transcript).
请注意，如果探针标识是唯一的非重复行被删除。这可能发生，如果出口从BeadStudio和/或ProbeID="TargetID"（“ProbeID”列有多个，在SampleProbeProfile“的唯一标识符，而”目标ID“不得指定”SampleGeneProfile“珠可以针对相同的成绩单）。
值----------Value----------
An ExpressionSetIllumina object.
ExpressionSetIllumina对象。
作者（S）----------Author(s)----------
Mark Dunning and Mike Smith
举例----------Examples----------
##Read the example data from[＃读取的数据为例]
##http://www.switchtoi.com/datasets/asuragenmadqc/AsuragenMAQC_BeadStudioOutput.zip[＃http://www.switchtoi.com/datasets/asuragenmadqc/AsuragenMAQC_BeadStudioOutput.zip]
##To follow this example, download the zip file [＃要按照这个例子中，下载的zip文件]
## Not run: [＃无法运行：]
dataFile = "AsuragenMAQC-probe-raw.txt"
qcFile = "AsuragenMAQC-controls.txt"
BSData = readBeadSummaryData(dataFile=dataFile, qcFile=qcFile, controlID="ProbeID",skip=0,qc.skip=0, qc.columns=list(exprs = "AVG_Signal"))
## 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。
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 2012-2-25 12:46:19
