processSwathData(beadarray)
processSwathData()所属R语言包：beadarray
Prepare iScan data for use with beadarray
准备为与beadarray使用ISCAN数据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Data from Illumina's newer iScan system come in a different format to the previous BeadScan data. This function is intended to transform the data into a format compatible with beadarray.
Illumina的新ISCAN系统的数据来自于不同的格式前BeadScan数据。此功能的目的是转换成数据，格式与beadarray兼容。
用法----------Usage----------
processSwathData(inputDir = NULL, outputDir = NULL, twoColour=NULL, textstring="_perBeadFile.txt", segmentHeight = 326, segmentWidth = 397, swathOverlap = 81, fullOutput = FALSE, newTextString=".txt", verbose = FALSE)
参数----------Arguments----------
参数：inputDir
Character string specifying the directory containing the data to be processed. If left NULL this defaults to the current working directory.
字符串指定目录中包含的数据进行处理。如果左NULL默认为当前工作目录。
参数：outputDir
Similar to the above, specifying the directory where the output should be written. If left NULL this defaults to the current working directory.
类似上述情况，指定输出应写入的目录。如果左NULL默认为当前工作目录。
参数：twoColour
Boolean value specifying whether the data is one or two channel. If left NULL the function will attempt to determing the number of channels be examing the files present in the directory.
布尔值，指定的数据是否是一个或两个通道。如果为NULL，函数将尝试测定通道数被追问目前目录中的文件。
参数：textstring
String specifying the suffix to identify the text file containing original bead-level data.
字符串，指定后缀识别的文本文件，其中包含原珠水平的数据。
参数：segmentHeight
Each array section is made up of several segments of beads, arranged in an hexagonal pattern. This value specifies the number of rows in a segment, and can be found in the accompanying .sdf file. In the future we will attempt to automate this.
每个阵列部分是由几个部分安排在一个六角形图案，珠。此值指定的段中的行数，与随行。sdf文件中可以找到。在未来，我们将尝试自动。
参数：segmentWidth
Similar to the above argument, this specifies the number of columns in an array segment.
类似上述说法，这个数组段中指定的列数。
参数：swathOverlap
Specifys the number of columns that appear in both swaths. Again this will hopefully be automated in the future.
Specifys出现在两个大片的列数。再次，这将有望在未来的自动化。
参数：fullOutput
Boolean value specifying the type of output. More details are given below.
布尔值，指定输出类型。下面给出更多细节。
参数：newTextString
Suffix for the two new "per swath" bead-level text file.
两个新的“每大片”珠级别的文本文件的后缀。
参数：verbose
Boolean value that, if TRUE, directs the function to print progress to the screen.
布尔值，如果属实，打印到屏幕上的进度指示功能。
Details
详情----------Details----------
Data from the iScan system comes with two images of each array section (along with two .locs files), which are labelled Swath1 and Swath2. These two images are of the two halves of the array section, with an overlapping region in the middle. However, there is only one bead-level text file, with no indication as to which of the two images each entry comes from. Given this, simply reading the bead-level text file will result in any function that uses bead locations performing undesirably.
从ISCAN系统的数据，配备两个图像的每个阵列部分（连同两个。LOCS文件），其中被标记Swath1和Swath2。这两个图像是数组段两部分，中间的重叠区域。但是，只有一个是珠级别的文本文件，有没有迹象显示每个条目来自两个图像。鉴于此，仅仅读珠级别的文本文件将导致任何使用珠地点进行不必要的功能。
This function works to try and deconvolute the bead-level data and create two files, one per swath, which can then be read independently into beadarray.
此功能和deconvolute珠级别的数据，并创建两个文件，每个大片之一，然后可以读入beadarray独立的。
The exact content of the output files depends upon the fullOutput argument. If the default value of FALSE is selected the function compares the coordinates in the "perBeadFile.txt" file with those found in the two .locs files, in order to determine which swath each bead is from. From this two new bead-level text files (with names containing "Swath1" and "Swath2" are created, containing all the beads from the orginal file. If the .locs files are not present this process will fail and the assigning of beads to swaths cannot be performed.
输出文件的确切内容取决于fullOutput参数。默认值FALSE被选中的功能比较的“perBeadFile.txt的”与那些发现在这两个文件的坐标。LOCS文件，以确定大片每个珠是从。来自这两个新珠级别的文本文件（与名称中含有“Swath1”和“Swath2”创建，从原价的文件包含所有的珠子。。LOCS文件不存在这一过程将失败和分配的大片珠不能执行。
If the fullOutput argument is set to TRUE both text files contain all the beads that can be identified in their respective images. Assuming that both the .locs and .tif files are present, we can use the bead-centre coordinates stored in the .locs files to calculate intensity values for beads in both images, even if no intensity is recorded Illumina's text file. Any bead that is found in the overlapping region, and thus appearing in both images, will have two intensities calculated. The files that are created contain the same data as regular bead-level text files, but with an additional column entitled "Weights". Beads that appear in both images are assigned a weight of 0.5 (since the are two intensity values for them), whilst all other beads are given a weigth of 1. If the TIFF images aren't available the intensities cannot be calculate, so the output will default to the same as if fullOutput = FALSE.
如果fullOutput参数设置TRUE两个文本文件包含所有的珠子可以在各自的图像识别。假设。LOCS。tif文件是存在的，我们可以使用珠中心存储协调。LOCS文件中的强度值来计算两个图像中的珠，即使没有强度记录Illumina的文本文件。任何被发现在重叠的区域，从而在两个图像出现的珠子，将有两个强度计算。创建定期珠级别的文本文件包含相同的数据，但有一个额外的列题为“砝码”的文件。出现在两个图像的珠被分配重量为0.5（因为是他们两个强度值），而所有其他珠子都获得了1自重。如果TIFF图像的强度无法计算的，所以输出将默认如果fullOutput = FALSE相同。
值----------Value----------
This function is called for its side effects, which is to produce two text files containing the beads match to the approriate swath. No value it returned by the function.
这个函数被调用，它的副作用，这是产生两个文本文件，其中包含的珠子相匹配的approriate大片。它由函数返回的值。
作者（S）----------Author(s)----------
Mike Smith and Andy Lynch
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 12:45:51
