readCel(affxparser)
readCel()所属R语言包：affxparser
Reads an Affymetrix CEL file
读取Affymetrix公司为CEL文件
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This function reads all or a subset of the data in an Affymetrix CEL file.
此功能读取所有或Affymetrix公司为CEL文件中的数据的一个子集。
用法----------Usage----------
readCel(filename,
indices = NULL,
readHeader = TRUE,
readXY = FALSE, readIntensities = TRUE,
readStdvs = FALSE, readPixels = FALSE,
readOutliers = TRUE, readMasked = TRUE,
readMap = NULL,
verbose = 0,
.checkArgs = TRUE)
参数----------Arguments----------
参数：filename
the name of the CEL file.
为CEL文件的名称。
参数：indices
a vector of indices indicating which features to read. If the argument is NULL all features will be returned.
表示要读哪些功能指标向量。如果参数是NULL的所有功能将被退回。
参数：readXY
a logical: will the (x,y) coordinates be returned.
一个逻辑：（X，Y）坐标将被退回。
参数：readIntensities
a logical: will the intensities be returned.
一个逻辑：将被退回的强度。
参数：readStdvs
a logical: will the standard deviations be returned.
一个逻辑：将被退回的标准偏差。
参数：readPixels
a logical: will the number of pixels be returned.
一个逻辑：将被退回的像素数。
参数：readOutliers
a logical: will the outliers be return.
逻辑：离群值会得到回报。
参数：readMasked
a logical: will the masked features be returned.
一个逻辑：将屏蔽功能，可以返回。
参数：readHeader
a logical: will the header of the file be returned.
一个逻辑：将文件头被退回。
参数：readMap
A vector remapping cell indices to file indices. If NULL, no mapping is used.
一个vector的重映单元指数提出的指标。如果NULL，没有映射。
参数：verbose
how verbose do we want to be. 0 is no verbosity, higher numbers mean more verbose output. At the moment the values 0, 1 and 2 are supported.
我们要如何详细进行。 0是没有冗长的，更高的数字意味着更详细的输出。此刻值0，1和2的支持。
参数：.checkArgs
If TRUE, the arguments will be validated, otherwise not. Warning: This should only be used if the arguments have been validated elsewhere!
如果TRUE，参数将被验证，否则不。警告：这应该只用于如果参数已在别处验证！
值----------Value----------
A CEL files consists of a header, a set of cell values, and information about outliers and masked cells.
一个CEL文件由一个头，一组单元格的值，离群和masked单元的信息。
The cell values, which are values extract for each cell (aka feature or probe), are the (x,y) coordinate, intensity and standard deviation estimates, and the number of pixels in the cell. If readIndices=NULL, cell values for all cells are returned, Only cell values specified by argument readIndices are returned.
单元格的值，这是值的每一个单元中提取（又名功能或探针），（X，Y）坐标，强度和标准差的估计，并在单元内的像素数量。 readIndices=NULL如果，所有单元的单元值返回，只有单元参数指定的值readIndices返回。
This value returns a named list with compontents described below:
此值返回与下面描述的分量命名名单：
参数：<code>header</code>
The header of the CEL file. Equivalent to the output from readCelHeader, see the documentation for that function.
CEL的文件头。相当于从readCelHeader，看到该函数的文档输出。
参数：x,y
(cell values) Two integer vectors containing the x and y coordinates associated with each feature.
（单元值）integerx和y坐标，每个功能的向量。
参数：<code>intensities</code>
(cell value) A numeric vector containing the intensity associated with each feature.
（单元格的值）numeric向量，与各功能相关的强度。
参数：stdvs
(cell value) A numeric vector containing the standard deviation associated with each feature.
（单元格的值）一个numeric向量与各功能相关的标准偏差。
参数：pixels
(cell value) An integer vector containing the number of pixels associated with each feature.
（单元格的值）integer向量每个功能的像素数。
参数：outliers
An integer vector of indices specifying which of the queried cells that are flagged as outliers. Note that there is a difference between outliers=NULL and outliers=integer(0); the last case happens when readOutliers=TRUE but there are no outliers.
integer指定查询的单元标记为离群指数的向量。注意：有一个outliers=NULL和outliers=integer(0)之间的差异;最后一种情况发生时readOutliers=TRUE但目前还没有离群。
参数：masked
An integer vector of indices specifying which of the queried cells that are flagged as masked. Note that there is a difference between masked=NULL and masked=integer(0); the last case happens when readMasked=TRUE but there are no masked features.
integer向量的指定查询的单元标记为掩盖指数。注意：有一个masked=NULL和masked=integer(0)之间的差异;最后一种情况发生时readMasked=TRUE但有没有屏蔽的功能。
The elements of the cell values are ordered according to argument indices. The lengths of the cell-value elements equals the number of cells read.
根据参数indices单元格值的元素是有序的。单元值元素的长度等于读取的单元数。
Which of the above elements that are returned are controlled by the readNnn arguments. If FALSE, the corresponding element above is NULL, e.g. if readStdvs=FALSE then stdvs is NULL.
由readNnn参数所传回的上述元素所控制。如果FALSE，上面对应的元素是NULL，例如：如果readStdvs=FALSE然后stdvs是NULL。
离群和蒙面单元----------Outliers and masked cells----------
The Affymetrix image analysis software flags cells as outliers and masked. This method does not return these flags, but instead vectors of cell indices listing which cells of the queried cells are outliers and masked, respectively. The current community view seems to be that this should be done based on statistical modelling of the actual probe intensities and should be based on the choice of preprocessing algorithm. Most algorithms are only using the intensities from the CEL file.
Affymetrix公司的图像分析软件标记单元异常和蒙面。此方法不返回这些标志，而不是向量的单元指数上市的质疑单元的单元异常和屏蔽，分别。当前社会的看法似乎是，这应该根据实际探测强度的统计模型和预处理算法的选择应基于。大部分算法只使用从CEL文件的强度。
内存使用----------Memory usage----------
The Fusion SDK allocates memory for the entire CEL file, when the file is accessed (but does not actually read the file into memory). Using the indices argument will therefore only affect the memory use of the final object (as well as speed), not the memory allocated in the C function used to parse the file. This should be a minor problem however.
融合的SDK分配整个CEL的文件，当文件被访问（但实际上并没有读取到内存中的文件）的内存。因此，使用indices参数将影响内存使用的最终目标（以及速度），而不是用来解析该文件的C函数分配的内存。这应该是一个小问题。
故障排除----------Troubleshooting----------
It is considered a bug if the file contains information not accessible by this function, please report it.
它被认为是一个错误，如果该文件包含此功能无法访问的信息，请报告。
作者（S）----------Author(s)----------
James Bullard, <a href="mailto:bullard@stat.berkeley.edu">bullard@stat.berkeley.edu</a> and Kasper
Daniel Hansen, <a href="mailto:khansen@stat.berkeley.edu">khansen@stat.berkeley.edu</a>
参见----------See Also----------
readCelHeader() for a description of the header output. Often a user only wants to read the intensities, look at readCelIntensities() for a function specialized for that use.
readCelHeader()头输出的描述。通常用户只想要阅读的强度，在readCelIntensities()寻找，使用专业功能。
举例----------Examples----------
for (zzz in 0) { # Only so that 'break' can be used[只有这样，“截断”可以用来]
# Scan current directory for CEL files[CEL文件扫描当前目录]
celFiles <- list.files(pattern="[.](c|C)(e|E)(l|L)$")
if (length(celFiles) == 0)
break;
celFile <- celFiles[1]
# Read a subset of cells[读单元的一个子集]
idxs <- c(1:5, 1250:1500, 450:440)
cel <- readCel(celFile, indices=idxs, readOutliers=TRUE)
str(cel)
# Clean up[清理]
rm(celFiles, celFile, cel)
} # for (zzz in 0)[（0 ZZZ）]
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 11:07:02
