readIllumina(beadarray)
readIllumina()所属R语言包：beadarray
Read bead-level Illumina data
阅读珠层次Illumina的数据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Reads bead-level ouput by Illumina's BeadScan software.
读取Illumina的BeadScan软件珠级别的输出中。
用法----------Usage----------
readIllumina(dir = ".", useImages = FALSE, illuminaAnnotation = NULL, sectionNames = NULL, metricsFile = "Metrics.txt", forceIScan = FALSE, dec = ".", ...)
参数----------Arguments----------
参数：dir
Directory from which to read the data, the default being the current working directory.
从中读取数据，默认为当前工作目录的目录。
参数：useImages
Boolean value specifying if bead intensities should be read directly from the source text files or calculated using the bead centre coordinates and image files. More details on the intensity calculation used are given below.
布尔值，指定如果珠强度应直接从源文本文件阅读或计算使用珠的中心坐标和图像文件。下面给出更多的细节上使用的强度计算。
参数：illuminaAnnotation
Character string specifiying the Illumina platform on which the data were generated. This is optional and will help to automate some analyses on expression data. Currently the choices for this argument are Humanv4, Humanv3, Humanv2, Humanv1, Mousev2, Mousev1, Mousev1p1, Ratv1.
字符串specifiying Illumina平台上产生的数据。这是可选的，将有助于自动化表达数据分析。目前，此参数的选择是Humanv4，Humanv3，Humanv2 Humanv1，Mousev2，Mousev1，Mousev1p1，Ratv1。
参数：sectionNames
Optional vector of character strings corresponding to section names to be read in. Typically these are the 10 digit numeric ID of Illumina chip followed by an underscore and capital letter
可选的对应部分的名字被读入的字符串矢量通常这些Illumina的芯片是10位数字ID由下划线和大写字母
参数：metricsFile
Optional name of a metrics file to be read in from the directory. Defaults to Metrics.txt. See details below for more information.
可选的指标名称的文件从目录中读取。默认到Metrics.txt。更多信息，详见下文。
参数：forceIScan
Only necessary for data from iScan machines. When TRUE, this argument forces beadarray to read data from files with the "perBeadFile.txt" extension, rather than seeking a file per swath. Use this if you are receiving the error "iScan data detected. This must first be processed with the function processSwathData()", but don't have access to .locs and .tif files for the array.
仅必要的ISCAN机的数据。当为true时，这个论点，迫使beadarray读与“perBeadFile.txt”的延伸，而不是寻求每大片文件，从文件中的数据。如果您收到错误“ISCAN检测数据。这首先必须处理的的功能processSwathData（）“，但没有访问。LOCS和TIF为阵列中的文件。
参数：dec
Decimal point character. This should be a character string containing just one single-byte character.
小数点字符。这应该是一个字符串，其中包含只有一个单字节字符。
参数：...
Other arguments to pass when reading bead-level text files.
其他参数传递阅读珠层次的文本文件时。
Details
详情----------Details----------
The bead-level data can be generated by any Illumina assay (expression, genotyping, methylation) and via BeadChips or Sentrix Array Matrix. However, some operations within the package are optimised for expression data. For optimal performance, BeadScan needs to be modified to output coordinates for each bead and to include outliers. See http://www.compbio.group.cam.ac.uk/Resources/illumina/index.html for details.
珠级别的数据，可以生成任何Illumina的检测（表达，基因分型，甲基化）和通过BeadChips或Sentrix阵列矩阵。然而，包内的一些操作进行了优化表达数据。为了获得最佳性能，需要进行修改，每个珠子BeadScan输出坐标，包括离群。见细节http://www.compbio.group.cam.ac.uk/Resources/illumina/index.html。
If present, the function will automatically read the following files from the directory
如果存在，该函数将自动读取从目录中的下列文件
.txt Text file that lists the ID, coordinates and intensity for every decoded bead on an array section. The intensities have been subjected to a local background correction. If useImages = FALSE these intensities will be used as a starting point for analysis
TXT文本文件，列出了每一个解码珠数组段的编号，坐标和强度。已受到当地背景校正的强度。如果useImages = FALSE这些强度将被用来作为分析的出发点
.sdf Illumina\'s Sample Description File for the entire chip or SAM. This is used within beadarray to determine the physical properties of a section.
自卫队Illumina的\s的取样描述整个芯片或SAM文件。这是用来确定一节物理性质，化学性质，在beadarray。
.locs Locations of all beads on the array (i.e. including all those that could not be decoded)
LOCS点阵列上（即包括所有那些不能被解码的所有珠）
Metrics.txt Illumina\'s metrics that are produced at the time of scanning. Identification of the Metrics file is defined by the metricsFile argument. Internally, this argument is passed to grep. The default will thus find other items such as "Metrics.txt2" or "OtherMetrics.txt". To avoid these being read you can use a more specific regex such as "^Metrics.txt$".
metrics.txt Illumina的\“在扫描时产生的指标。 metricsFile参数定义的度量文件的鉴定。内部，这个参数被传递到grep。因此，默认会找到其他项目，如的“Metrics.txt2”或“OtherMetrics.txt”。为了避免这些被读取，你可以使用如“^ Metrics.txt $”更具体的regex。
Separate functionality exists to read and manipulate TIFF images that may be found in the same directory. See readTIFF.
存在单独的功能来读取和处理，可在同一目录中发现的TIFF图像。看到readTIFF。
If useImage is set to TRUE, intensities are extracted from the TIFF images using the bead-centre coordinates provided in the text file. Foreground values are calculated from a sharpened version of the image as described in Kuhn et al. Background values are calculated as the median of the 5 lowest pixels in a 17x17 pixel square around the bead-centre, detailed in Smith et al.
如果useImage设置为TRUE，强度使用珠中心坐标在文本文件中所提供的TIFF图像中提取。从库恩等人所述的图像锐化版本的前景值计算。在一个17x17像素的正方形最低5像素左右珠中心详细史密斯等人，中位数作为背景值计算。
值----------Value----------
Returns an object of class beadLevelData-class
返回一个对象的类beadLevelData-class
作者（S）----------Author(s)----------
Mike Smith, Mark Dunning, Andy Lynch
参考文献----------References----------
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。
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发表于 2012-2-25 13:05:46
