getLocalProbeIntensities(GeneRegionScan)
getLocalProbeIntensities()所属R语言包：GeneRegionScan
Get Probe Intensities locally
在本地获取探针强度
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Function that will create a ProbeLevelSet from cel files.
功能，将创建1 ProbeLevelSet CEL文件。
用法----------Usage----------
getLocalProbeIntensities(listOfProbesets, celfilePath, annotation=NULL, aptCelExtractPath=NULL, pgfPath=NULL, clfPath=NULL,
cdfPath=NULL, verbose=TRUE)
参数----------Arguments----------
参数：listOfProbesets
Either a character vector with the names of the probesets from which probes should be included in the ProbeLevelSet, or the path name of a file containing this
无论是从探针应列入ProbeLevelSet的probesets的名称的字符向量，或一个包含这个文件的路径名称
参数：celfilePath
The path to a folder that contains the cel files of interest.
到一个文件夹，其中包含利息CEL文件的路径。
参数：annotation
Character string specifying which type of arrays is investigated.
字符串指定调查的是哪种类型的数组。
参数：aptCelExtractPath
The path to the apt-cel-extract file from the Affymetrix Power Tools package (including the filename itself). You can try to leave it as NULL and see what happens. If the tool is in path, it will work anyway. If you have specified the argument before it will be remembered. If you are using an OS for which executables have been included in the package (win32 and linux64), it will use that.
从Affymetrix公司的电动工具包（包括文件名本身）的apt-CEL提取文件的路径。你可以尝试离开它为NULL，并看看会发生什么。如果刀具路径是，它无论如何都会正常工作。如果你已经指定的参数，然后将记住它。如果您使用的是其中的可执行文件已包含在包（WIN32与Linux64）的操作系统，它将使用。
参数：pgfPath
The path to a pgf file for the exon array of interest. This argument is mutually exclusive with the cdfPath argument. These files can be downloaded from www.affymetrix.com for the array of interest. Once given for a particular annotation, the location is saved for future use and can be given as NULL next time.
为利益的外显子阵列的PGF文件的路径。这种说法是与cdfPath参数互相排斥的。这些文件可以下载从www.affymetrix.com的阵列利益。一旦给定一个特定的注解，以供将来使用保存的位置，并可以为NULL下一次。
参数：clfPath
The path to a clf file for the exon array of interest. This argument is mutually exclusive with the cdfPath argument. These files can be downloaded from www.affymetrix.com for the array of interest. Once given for a particular annotation, the location is saved for future use and can be given as NULL next time.
clf文件的利息外显子阵列的路径。这种说法是与cdfPath参数互相排斥的。这些文件可以下载从www.affymetrix.com的阵列利益。一旦给定一个特定的注解，以供将来使用保存的位置，并可以为NULL下一次。
参数：cdfPath
The path to a cdf file for the array of interest. This argument is mutually exclusive with the pgfPath and clfPath arguments. These files can be downloaded from www.affymetrix.com for the array of interest. Once given for a particular annotation, the location is saved for future use and can be given as NULL next time.
CDF文件的路径为阵列的利益。这种说法是与pgfPath和clfPath参数相互排斥。这些文件可以下载从www.affymetrix.com的阵列利益。一旦给定一个特定的注解，以供将来使用保存的位置，并可以为NULL下一次。
参数：verbose
TRUE or FALSE.
TRUE或FALSE。
Details
详情----------Details----------
This is the workhorse function for generating ProbeLevelSets. It has two main functions: 1) It extracts the probe level intensity, normalizes it to all probes in the data using quantiles normalization and transfers the results to the exprs part of a ProbeLevelSet. The extraction and normalization parts are done by a call to the Affymetrix Power Tools (APT) function apt-cel-extract. The analysis switch for this call is '-a quant-norm,pm-only' and the documentation for APT can be used for further reference. 2) It extracts the probe sequences of all probes of interest. This is done using the [arrayname]probe packages for the 3'IVT type arrays for which they are available. For the exon type arrays, for which this is not available it is done by direct parsing of the pgf
这是产生ProbeLevelSets的主力功能。它有两个主要功能：1）提取探针强度，标准化的数据位数标准化所有探针和传输到一个ProbeLevelSet exprs部分成果。调用的Affymetrix公司的电动工具（APT）的功能APT-CEL提取物的提取和标准化的部分。这一呼吁的分析开关是一个定量的规范，仅下午和APT的文件可以进一步参考使用。 2）提取所有感兴趣的探针，探针序列。这样做是为3IVT类型的阵列，为他们提供使用[ARRAYNAME]探测包。为外显子类型的数组，这是没有的，它是通过直接解析的PGF
值----------Value----------
A ProbeLevelSet with probe intensity values for all probes in the specified probesets. The ProbeLevelSet
具有，为在指定probesets的所有探针的探针强度值ProbeLevelSet。在ProbeLevelSet
作者（S）----------Author(s)----------
Lasse Folkersen
参见----------See Also----------
getServerProbeIntensities, plotOnGene
getServerProbeIntensities，plotOnGene
举例----------Examples----------
## Not run: [＃无法运行：]
#must correct paths and give cel files before this example will work[必须正确的路径和CEL文件，在此之前的例子将工作]
listOfProbesets<-c("10321_at")
celfilePath<-path_to_some_cel_files
aptCelExtractPath<-"~/apt/apt-cel-extract"
cdfPath<-"~/hgu133plus2.cdf"
getLocalProbeIntensities(listOfProbesets, celfilePath, annotation="hgu133plus2", aptCelExtractPath=aptCelExtractPath, cdfPath=cdfPath)
## 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 18:58:40
