read.SnpSetIllumina(beadarraySNP)
read.SnpSetIllumina()所属R语言包：beadarraySNP
Read Experimental Data, Featuredata and Phenodata into an 'SnpSetIllumina' Object
读入一个SnpSetIllumina对象的实验数据，Featuredata和Phenodata
译者：生物统计家园网 机器人LoveR
描述----------Description----------
A SnpSetIllumina object is created from the textfiles created by the Illumina GenCall or BeadStudio software.
从Illumina公司GenCall或BeadStudio软件创建的文本文件创建一个SnpSetIllumina对象。
用法----------Usage----------
read.SnpSetIllumina(samplesheet, manifestpath=NULL, reportpath=NULL,
rawdatapath=NULL, reportfile=NULL, briefOPAinfo=TRUE, readTIF=FALSE,
nochecks=FALSE, sepreport="\t", essentialOnly=FALSE, ...)
参数----------Arguments----------
参数：samplesheet
a data.frame or filename, contains the sample sheet
数据框或文件名，包含示例表
参数：manifestpath
a character string for the path containing the manifests / OPA definition files, defaults to path of samplesheet
一个包含舱单/ OPA的定义文件，默认路径samplesheet路径字符串
参数：reportpath
a character string for the path containing the report files, defaults to path of samplesheet
一个报告文件，默认包含路径samplesheet路径字符串
参数：rawdatapath
a character string for the path containing the intensity data files, defaults to path of samplesheet
一个包含强度的数据文件，默认路径samplesheet路径字符串
参数：reportfile
a character string for the name of BeadStudio reportfile
为BeadStudio reportfile名称的字符串
参数：briefOPAinfo
logical, if TRUE then only the SNP name, Illumi code, chromosome and basepair position are put into the featureData slot of the result, else all information from the OPA file is put into the featureData slot
逻辑，如果TRUE到featureData结果插槽SNP的名称，ILLUMI代码，染色体，碱基对的位置，否则从OPA文件的所有信息放到featureData 插槽
参数：readTIF
logical, uses beadarray package and raw TIF files to read data
逻辑，使用beadarray包和原始TIF文件读取数据
参数：nochecks
logical, limited validity checks on beadstudio report files. See details
逻辑，有限的有效性检查对beadstudio报告文件。查看详情
参数：sepreport
character, field separator character for beadstudio report files
字符，现场为beadstudio报告文件分隔符
参数：essentialOnly
logical, if TRUE then only the essential columns from a reportfile are included into the result. See details
逻辑，如果TRUE然后只有从reportfile的基本列包含到结果。查看详情
参数：...
arguments are forwarded to readIllumina and can be used to perform bead-level normalization
参数转发到readIllumina可以用来执行珠标准化
Details
详情----------Details----------
The text files from Illumina software are imported to a SnpSetIllumina object. Both result files from GenCall and BeadStudio can be used. In both cases the sample sheets from the experiments are used to select the proper data from the report or data files. The following columns from the sample sheet file are used for this purpose: "Sample_Name", "Sentrix_Position", and "Pool_ID". The values in columns "Sample_Plate", "Pool_ID", and "Sentrix_ID" should be the same for all samples in the file, as this is the case for processed experiments. The contents of the sample sheet are put into the phenoData slot.
从Illumina公司软件的文本文件导入到SnpSetIllumina对象。两个结果从GenCall和BeadStudio文件都可以使用。在这两种情况下，从实验样品表用于选择正确的数据报告或数据文件。下面列从样品表文件用于这一目的：Sample_Name，Sentrix_Position，Pool_ID。在值列Sample_Plate，Pool_ID，Sentrix_ID应该是文件中的所有样品相同，因为这种情况下处理实验。样品表的内容被放到phenoData插槽。
Zero values in the raw data signals are set to NA
在原始数据信号的零值设置为NA
Ideally the OPA manifest file containing SNP annotation should be available, these files are provided by Illumina. Columns "IllCode", "CHR", and "MapInfo" are put into the featureData slot.
理想OPA的manifest文件包含的SNP注解应该是可用的，这些文件是由Illumina公司提供。列IllCode，CHR，MapInfofeatureData插槽。
GenCall Data
GenCall数据
In order to process experiments that were genotyped using the GenCall software, the arrays should be scanned with the setting <SaveTextFiles>true</SaveTextFiles> in the Illumina configuration file Settings.XML. 3 Types of files need to be present in the same folder: The sample sheet, .csv files containing signal intensity data, and the report file that contains the genotype information. For each sample in the sample sheet there should be a .csv file with the following file mask: [sam_id]_R00[yy]_C00[xx].csv, where sam_id is the Illumina ID for the SAM, and xx and yy are the column and row number respectively. From the report files the file with mask [Pool_ID]_LocusByDNA[_ExpName].csv is used. "Pool_ID" is the OPA panel used, and "_ExpName" is optional.
为了处理实验基因型使用GenCall软件，阵列应设置<SaveTextFiles>true</SaveTextFiles>在Illumina的配置文件Settings.XML扫描。 3文件类型必须是目前在同一文件夹中：样品表，CSV文件包含信号强度数据，报告文件，其中包含的基因型信息。对于每个样品在样品表应该与csv文件下列文件掩码：[sam_id]_R00[yy]_C00[xx].csv，sam_id是Illumina的编号为SAM，xx和<X >是分别列和行数。从报告文件的文件面具yy使用。 [Pool_ID]_LocusByDNA[_ExpName].csv是使用OPA的面板，和Pool_ID是可选的。
BeadStudio Data
BeadStudio数据
To process experiments that were processed with BeadStudio, only two files are needed. The sample sheet and the Final Report file. The sample sheet must contain the same columns as for GenCall, the report file should contain the following columns: "SNP Name", "Sample ID", "GC Score", "Allele1 - AB", "Allele2 - AB", "GT Score", "X Raw", and "Y Raw". "SNP Name" and "Sample ID" are used to form rows and columns in the experimental data, "GC Score" is put in the callProbability matrix, "Allele1 - AB" and "Allele2 - AB" are combined into the call matrix, "GT Score" is added to the featureData slot, "X Raw" is put in the R matrix and "Y Raw" in the G matrix. Other columns in the report file are added as matrices in the assayData slot, or columns in the featureData slot if values are identical for all samples in the reportfile. When nochecks is TRUE then only the "SNP Name" and "Sample ID" columns are required. The resulting object is now of class MultiSet
为了处理实验处理BeadStudio，只有两个文件是必要的。样品表和最终报告文件。样品表必须包含相同的列，为GenCall的，报告文件应包含以下几列：SNP Name，Sample ID，GC Score Allele1 - AB，Allele2 - AB，GT Score，X Raw，Y Raw＆rsquo ; SNP Name和Sample ID是用来形成行和列中的实验数据，“GC ScorecallProbability的矩阵，Allele1 - AB和Allele2 - ABcall矩阵，组合成GT ScorefeatureData插槽X RawR矩阵和Y RawG矩阵。如果值是在reportfile所有样品相同，增加一条，作为矩阵assayData插槽，或featureData插槽列在报告文件中的其他列。当nochecks是TRUE然后只SNP Name和Sample ID列。现在产生的对象是类MultiSet
Sample sheets
样品表
To help generate a sample sheet for BeadStudio data a Sample_Map.txt file can be converted to a sample sheet with the Sample_Map2Samplesheet function. For Beadstudio reportfiles it is also possible to set samplesheet=NULL. In this case the phenoData slot will be fabricated from the sample names in the reportfile.
为了帮助BeadStudio数据生成样品表1 Sample_Map.txt文件Sample_Map2Samplesheet函数可以转换成一个示例表。对于Beadstudio reportfiles它也可以设置samplesheet =NULL。在这种情况下phenoData槽将在reportfile样本名捏造。
Manifest/OPA/annotation files
列表/ OPA的/注释文件
For BeadStudio reportfiles it is not necessary to have a Manifest file if the columns "Chr" and "Position" are available in the report file. Currently this is the only way to import data from Infinium arrays, because Illumina does not supply Manifest files for these arrays.
对于BeadStudio reportfiles，它有一个manifest文件，如果是没有必要的列Chr和Position在报告文件中。这是目前唯一的方式导入Infinium阵列的数据，因为Illumina公司不提供这些阵列Manifest文件。
值----------Value----------
This function returns an SnpSetIllumina object, or a MultiSet object when nochecks is TRUE.
这个函数返回一个SnpSetIllumina对象，或MultiSet时nochecks是TRUE的对象。
作者（S）----------Author(s)----------
Jan Oosting
参见----------See Also----------
SnpSetIllumina-class, Sample_Map2Samplesheet, readIllumina
SnpSetIllumina-class，Sample_Map2Samplesheet，readIllumina
举例----------Examples----------
# read a SnpSetIllumina object using example textfiles in data directory[读SnpSetIllumina对象，例如文本文件在数据目录]
datadir <- system.file("testdata", package="beadarraySNP")
SNPdata <- read.SnpSetIllumina(paste(datadir,"4samples_opa4.csv",sep="/"),datadir)
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 12:37:02
