microarray2soft(GEOsubmission)
microarray2soft()所属R语言包：GEOsubmission
Prepares microarray data for submission to GEO
准备提交到地球同步轨道的芯片数据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Converts a microarray dataset and the corresponding sample information
转换芯片集和相应的样品信息
用法----------Usage----------
microarray2soft(samplenames, sampleinfo, seriesnames, seriesinfo,
datadir=NULL, infodir=NULL, writedir=NULL, softname=NULL,
参数----------Arguments----------
参数：samplenames
character vector. Sample names.
特征向量。样本名。
参数：sampleinfo
character string. Name of a tab-delimited file with sample information. Each line in the file corresponds to a sample. Sample names are stored under column header SAMPLE. Other column headers will be looked up for a match against the sample labels required by the SOFT format.
字符串。与样本信息的制表符分隔的文件的名称。文件中的每一行对应一个样本。样品名称存储在列标题样品。其他列标题将抬头对软格式所需样品标签匹配。
参数：seriesnames
charcter vector. Series name. Works only with 1 series at present time.
charcter向量。系列名称。仅适用于目前的时间与1系列。
参数：seriesinfo
character string. Name of a tab-delimited file with series information. Only 1 line (ie. 1 series) allowed at present time (in addition to the header). Series names are stored under column header SERIES. Other column headers will be looked up for a match against the series labels required by the SOFT format.
字符串。一个系列信息的制表符分隔的文件的名称。只有1号线（即1系列）在目前的时间允许（头）。系列名称都存储在列标题系列。其他列标题将抬头对软格式所需的系列标签匹配。
参数：datadir
character string. Name of the directory (with associated path) containing the microarray data files. Defaults to the working directory.
字符串。含有芯片的数据文件的目录的名称（与关联路径）。默认工作目录。
参数：infodir
character string. (Full path to) Directory containing the text file with sample info (sampleinfo) and series info (seriesinfo). Defaults to datadir.
字符串。 （完整路径）目录包含的样本信息（sampleinfo）的系列信息（seriesinfo）的文本文件。 DATADIR默认。
参数：writedir
character string. (Full path to) Directory to write the SOFT file to. Defaults to datadir.
字符串。 （完整路径）目录写的软文件。 DATADIR默认。
参数：softname
character string. SOFT file name. Defaults to the name of the series info file, with suffix .soft. If "", print to the standard output connection.
字符串。软文件名。默认系列info文件的名称，后缀。软。如果“”打印到标准输出连接。
参数：expressionmatrix
character string. Name of a tab-delimited text file with normalized expression values, by default in datadir (but if the string contains "/", it is considered a full path and it is read or written at the corresponding location). If expressionmatrix is non-null and a corresponding file exists, it is used as the source of gene expression values to be written in the SOFT file. Column names in this file should match the names of raw data files given in sampleinfo. If expressionmatrix is non-null but no corresponding file is found, normalized expression values calculated from the microarray data files (only Affymetrix CEL files at the moment) are written to this file.
字符串。一个规范化的表达值由在DATADIR默认，但如果字符串中包含“/”，它被认为是一个完整的路径，它是唯读或写在相应的位置的制表符分隔的文本文件的名称。 ，如果expressionmatrix非空和相应的文件存在，它是用来在软文件的书面源基因的表达值。在这个文件中的列名应符合在sampleinfo给出的原始数据文件的名称。如果的expressionmatrix非空，但没有找到相应的文件，规范化表达芯片的数据文件（Affymetrix公司为CEL文件的时刻）计算值被写入这个文件。
参数：verbose
logical. If FALSE suppress all messages (useful to write the SOFT file to standard output). Defaults to TRUE.
逻辑。如果为FALSE抑制所有消息（有用的写软文件到标准输出）。默认为true。
Details
详情----------Details----------
Converts a microarray dataset and the corresponding sample information into a SOFT file that is ready to be used for direct deposit into GEO.
转换芯片集和成软的文件，是随时可以使用直接存款进入地球的相应的样品信息。
Sample information and series information are taken from two separate plain text files. The column names in these two files should match the labels defined by the SOFT format (see http://www.ncbi.nlm.nih.gov/geo/info/soft2.html). This allows for the extraction of the information needed to write the SOFT format file.
从两个独立的纯文本文件，样品信息和正在采取的一系列信息。这两个文件中的列名应符合软格式（见http://www.ncbi.nlm.nih.gov/geo/info/soft2.html）定义的标签。这使得写软格式的文件所需的信息提取。
Currently only a subset of SOFT keywords are accepted but they are expected to suffice for standard submissions (in particular for 1-color microarrays).
目前只有软关键字的子集被接受，但他们预计将足以为标准的意见书（特别是在1色芯片）。
Normalized expression values are read from a tab-delimited file. Alternatively, in the case of an Affymetrix dataset, raw microarray data files (CEL files) can be processed directly (they are RMA-normalized) and written to the SOFT file.
规范化表达读取值由制表符分隔的文件。另外，在一个Affymetrix公司的数据集的情况下，原始芯片的数据文件（CEL文件）可以直接处理（他们是标准化的RMA）和软文件写入。
See the example below or the vignette for the format of sampleinfo, seriesinfo and expressionmatrix.
见下面的例子或，格式sampleinfo，seriesinfo和expressionmatrix的小插曲。
注意----------Note----------
The SOFT file format is defined at
软文件格式定义
作者（S）----------Author(s)----------
Alexandre Kuhn, kuhnam@mail.nih.gov
举例----------Examples----------
##location of example files for sampleinfo and seriesinfo (i.e. provided[＃位置为例如sampleinfo和seriesinfo文件（即提供]
##with this vignette)[＃这个小插曲）]
dataDirectory <- system.file(package='GEOsubmission', 'extdata')
## Define a directory and a file to write the generated example SOFT[＃定义一个目录和文件的编写生成例如软]
## file out to (for the sake of this demo) [＃文件（为了这个演示）]
soft_example_fullpath <- tempfile(pattern='soft_example')
soft_example_name <- basename(soft_example_fullpath)
soft_example_dir <- dirname(soft_example_fullpath)
## Example with a dataset (series) named "neuronalCultures", comprised[＃示例名为“neuronalCultures”，其中包括数据集（系列）]
## of 2 samples (named "1" and "2")[＃2样品（命名为“1”和“2”）]
## This example is not run since the CEL files corresponding to sample[＃这个例子是不是运行以来CEL文件相应的采样]
## "1" and "2" (and indicated in "sampleInfo.txt") do not exist (which[＃“1”和“2”（表示在“sampleInfo.txt”）不存在（]
## would be purposedly detected by microarray2soft and cause it to[＃将被刻意由microarray2soft检测，并使其]
## stop). [＃停止）。]
## Not run: [＃无法运行：]
microarray2soft(c('1','2'), 'sampleInfo.txt', 'neuronalCultures',
'seriesInfo.txt', datadir=dataDirectory,
writedir=soft_example_dir, softname=soft_example_name)
## End(Not run)[＃结束（不运行）]
## The files "sampleInfo.txt" (as sampleInfo) and "seriesInfo.txt" (as[＃文件“sampleInfo.txt”（sampleInfo）和“seriesInfo.txt”（如]
## seriesInfo) are provided as example files in the "extdata" directory of[＃seriesInfo）提供例如文件中的“extdata”目录]
## the package installation directory. Their content can be printed to the[＃包的安装目录。其内容可以打印到]
## R console with [＃R控制台]
## Not run: [＃无法运行：]
dataDirectory<-system.file(package='GEOsubmission','extdata')
read.delim(file.path(dataDirectory,'sampleInfo.txt'))
read.delim(file.path(dataDirectory,'seriesInfo.txt'))
## End(Not run)[＃结束（不运行）]
## Example specifying a separate file containing normalized expression[＃示例指定一个单独的文件，包含标准化的表达]
## values (here the example file "expressionNormalized.txt") [＃值（例如文件“expressionNormalized.txt”）]
microarray2soft(c('1','2'), 'sampleInfo.txt', 'neuronalCultures',
'seriesInfo.txt', datadir=dataDirectory,
writedir=soft_example_dir, softname=soft_example_name,
expressionmatrix='expressionNormalized.txt')
## The file "expressionNormalized.txt" (as expressionmatrix) is provided[＃文件“expressionNormalized.txt”（作为expressionmatrix）]
## as example file in the "extdata" directory of the package installation[＃作为示例文件包安装目录的“extdata”]
## directory. It can be printed to the R console with [＃目录。它可以印刷的R控制台]
## Not run: [＃无法运行：]
dataDirectory<-system.file(package='GEOsubmission','extdata')
read.delim(file.path(dataDirectory,'expressionNormalized.txt')
## End(Not run)[＃结束（不运行）]
## Same as the preceding example but write the example SOFT file to the[＃前面的例子相同，但写的例子软文件]
##console (note the use of verbose=FALSE to suppress messages) [＃控制台（注意使用VERBOSE = FALSE抑制消息）]
microarray2soft(c('1','2'), 'sampleInfo.txt', 'neuronalCultures',
'seriesInfo.txt', datadir=dataDirectory,
softname='', expressionmatrix='expressionNormalized.txt',
verbose=FALSE)
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 19:41:45
