load.abi(TRAMPR)
load.abi()所属R语言包：TRAMPR
Load ABI Output Files
加载ABI输出文件。
译者：生物统计家园网 机器人LoveR
描述----------Description----------
These functions help convert data from Applied Biosystems Gene Mapper (ABI) output format into TRAMPsamples objects for analysis. Note that this operates on the summarised output (a text file), rather than the .fsa files containing data for individual runs.
这些功能可以帮助从美国应用生物系统公司（ABI）基因映射输出格式的数据转换成TRAMPsamples对象进行分析。请注意，此操作概要输出（文本文件），而不是.fsa含有单独运行的数据的文件。
Details of the procedure of this function are given below, and a worked example is given in the package vignette; type vignette("TRAMPRdemo") to view it.
此功能的程序的详情，工作的例子是包中的小插曲;类型vignette("TRAMPRdemo")观看。
The function peakscanner.to.genemapper is an experimental function to convert from peakscanner output to abi genemapper output. The peakscanner output is very slightly different in format, and currently load.abi is very fussy about the input file's structure. Eventially load.abi will be made more tolerant, but as an interim solution, run peakscanner.to.genemapper on your file. By default, running peakscanner.to.genemapper(myfile.csv) will produce a file myfile.txt. This can then be loaded using load.abi as described below, specifying myfile.txt as the file argument.
函数peakscanner.to.genemapper是一个实验性的功能，以转换从peakscanner输出ABI genemapper输出。 peakscanner输出略有不同的格式，目前load.abi是很挑剔的输入文件的结构。 Eventially load.abi将变得更加宽容，但作为一个临时解决方案，运行peakscanner.to.genemapper了您的文件。默认情况下，运行peakscanner.to.genemapper(myfile.csv)会产生一个文件myfile.txt。然后可以加载使用load.abi如下文所述，指定myfile.txtfile参数。
用法----------Usage----------
load.abi(file, file.template, file.info, primer.translate, ...)
load.abi.create.template(file, file.template)
load.abi.create.info(file, file.template, file.info)
peakscanner.to.genemapper(filename, output)
参数----------Arguments----------
参数：file
The name of the file from which the ABI data are to be read from.
ABI的数据是要读取的从从该文件的名称。
参数：file.template
The name of the file containing the “template” file (see Details).
名的文件，其中包含的“模板”文件（见详情）。
参数：file.info
(Optional) the name of the file containing extra information associated with each sample (see Details).
（可选）的名称，该文件包含额外的相关信息，每个样品（见详情）。
参数：primer.translate
List used to translate dye codes into primers. The same codes are assumed to apply across the whole file. See Details for format.
列出用于染料的代码翻译成引物。相同的代码被假定为适用于整个文件。请参阅格式的详细信息。
参数：...
Additional objects to incorportate into a TRAMPsamples object. See TRAMPsamples for details.
额外的的对象的incorportate成TRAMPsamples对象。见TRAMPsamples的详细信息。
参数：filename
In peakscanner.to.genemapper, the name of the csv file containing output.
在peakscanner.to.genemapper，包含输出的csv文件的名称。
参数：output
In peakscanner.to.genemapper, the name of the file to be output in abi format (if omitted, this will be automatically generated).
在peakscanner.to.genemapper，的文件的文件名，以是在阿比格式的输出（如果省略，这将自动生成）。
Details
详细信息----------Details----------
Some terminology: a “sample” refers to a physical sample (e.g. a root tip), while a “run” refers to an individual TRFLP run (i.e. one enzyme and one primer). Because two primers are run at once, each “runfile” contains information on two “runs”, but each “sample” may contain more than one “runfile”. Runfiles are distinguished by different sample.file.name values in the ABI file, while different samples are distinguished by different sample.fk/sample.pk values.
一些术语：“样品”是指一个物理样品（例如根小费），而一个“运行”是指个别TRFLP运行（即一种酶和一种引物）。由于两个引物中运行一次，每个“RUNFILE”包含两个“奔跑”的信息，但可能包含一个以上的的“RUNFILE”每个“样本”。的Runfiles来区分不同的sample.file.name值在ABI文件，同时区分不同样品的不同sample.fk/sample.pk值。
primer.translate is a list used to translate between the dyes recorded in the ABI file and the primers used. Each element corresponds to a different primer, and is a vector of different colour dyes. The list:
primer.translate是用来翻译在ABI文件和使用的引物之间的染料记录列表。每个元素对应于一个不同的引物，并是一个向量，不同颜色的染料。该列表：
list(ITS1F="B", ITS4="G")
list(ITS1F="B", ITS4="G")
would translate all dyes with the value "B" to "ITS1F", and all dyes with the value "G" to "ITS4". The list:
把所有染料的价值"B"到"ITS1F"，和所有染料的价值"G"到"ITS4"。该列表：
list(ITS1F="B", ITS4=c("G", "Y"))
list(ITS1F="B", ITS4=c("G", "Y"))
would do the same, except that both "G" and "Y" dyes would be converted to "ITS4". If a dye is used in the data that is not represented within primer.translate, then it will be excluded (e.g., all rows of data with dye as "R" will be excluded).
会做相同的，除了这两个"G"和"Y"染料会被转换为"ITS4"。如果使用染料中的数据是不内表示primer.translate，然后它会被排除在外（例如，所有的数据行dye的"R"会被排除在外）。
The procedure for loading in ABI data is:
装载在ABI数据的过程是：
Create the “template” file. Template files are required to record which enzymes were used for each run, since that is not included in the ABI output, and to group together separate runs (typically different enzymes) that apply to the same individual. The function load.abi.create.template will create a template that contains all the unique file names found in the ABI file (as sample.file.name), and blank columns titled enzyme and sample.index. Running
创建“模板”文件。模板文件都需要记录的酶被用于每个运行，因为这是不包括在ABI输出，并组合到一起，适用于同一个人的单独运行（通常是不同的酶）。函数load.abi.create.template将创建一个模板，它包含所有唯一的文件名在ABI文件（sample.file.name），和空白标题为enzyme和sample.index。运行
load.abi.create.template(x)
load.abi.create.template(x)
where x is the name of your ABI file will create a template file in the same directory as the ABI file. The function will print the name and location of the template file to the console.
x是ABI文件的名称将创建一个模板文件的ABI文件在同一目录下。该函数将打印到控制台的模板文件的名称和位置。
Edit the template file and save. The enzyme and sample.index columns are initially empty and need filling in, which can be done in Excel, or another spreadsheet program. The sample.index column links sample.file.name back to an individual sample; multiple sample.file.names that share sample.index values come from the same individual sample. (If editing with Excel, ignore all the warnings about incompatible file formats when saving.) sample.index should be a positive integer (but see Note below).
编辑该模板文件并保存。 enzyme和sample.index列初始为空，需要填写，可以在Excel或其他电子表格程序。 sample.index列链接sample.file.name：“单个样品，多sample.file.name的份额sample.index值来自同一个体的样本。 （如果使用Excel编辑，忽略所有的警告不兼容的文件格式保存时。）sample.index的应该是一个正整数（见下文附注）。
Optionally create an “info” file, which is useful if you want to associate extra information against your samples. The function load.abi.create.info will create an info file that contains all the unique values of sample.index, and an empty column titled species. The species column can be filled in where the species is known (e.g. from collections of sporocarps). Any additional columns may be added. Running
（可选）创建一个“信息”的文件，该文件是有用的，如果你想关联的额外信息对您的样品。的功能load.abi.create.info将创建一个信息文件，该文件包含所有的独特价值sample.index，和一个空列名为species。 species栏可以填写该物种被称为（例如集合子实体）。任何额外的列可能会增加。运行
load.abi.create.info(x)
load.abi.create.info(x)
where x is the name of your ABI file will create an info file in the same directory as the ABI file. The function will print the name and location of the info file to the console. Edit and save this file.
x ABI文件的名称将ABI文件在同一目录下创建一个信息文件。该函数将打印到控制台的信息文件的名称和位置。编辑并保存该文件。
Create the TRAMPsamples object by running load.abi. This loads your ABI data, plus the new template file, plus an optional information file. Running
创建运行TRAMPsamplesload.abi对象。这将加载您的ABI的数据，再加上新的模板文件，以及一个可选的信息文件。运行
my.samples <- load.abi(x, primer.translate=primer.translate)
my.samples <- load.abi(x, primer.translate=primer.translate)
will create an object “my.samples” containing your data.
将创建一个对象“my.samples”，其中包含您的数据。
By default, the filenames of the template and info files will be automatically generated: <prefix>.<ext> becomes <prefix>_template.csv or <prefix>_info.csv. If you choose to specify file.template or file.info manually when running load.info.create.template or load.info.create.info, you must use the same values of file.template and file.info when running load.abi.
默认情况下，将自动生成的模板和信息文件的文件名：<prefix>.<ext><prefix>_template.csv或<prefix>_info.csv。如果您选择指定file.template或file.info手动运行时load.info.create.template或load.info.create.info，您必须使用相同的值file.template和file.info运行load.abi。
警告----------Warning----------
Do not change the names of any columns produced by load.abi.create.template or load.abi.create.info.
不要更改产生的任何列load.abi.create.template或load.abi.create.info的名称。
注意----------Note----------
There is no reason that data from other types of output files could not be manually imported using TRAMPsamples. We welcome contributions for other major data formats.
没有任何理由，其他类型的输出文件的数据不能被手动导入使用TRAMPsamples。我们欢迎其他主要的数据格式的贡献。
When creating sample.index values, these should be positive integers. If you enter strings (e.g. a1, b1), these will be automatically converted into integers. Once loaded, sample.pk/sample.fk is always a positive integer key, but sample.index will be retained as your string keys.
当创建“sample.index值，这些应为正整数。如果输入的字符串（如：a1，b1），它们将被自动转换成整数。一旦加载，sample.pk/sample.fk是一个正整数键，但将保留为sample.index字符串键。
参见----------See Also----------
read.abi, which reads in ABI data with few modifications.
的read.abi，读取ABI很少修改的数据。
TRAMPsamples, which documents the data type produced by load.abi.
TRAMPsamples，它记录的数据类型产生的load.abi。
The package vignette, which includes a worked example of loading data using these functions; to locate the vignette, type help(library=TRAMPR), and scroll to the bottom of the page, or type: system.file("doc/TRAMPR_demo.pdf", package="TRAMPR").
包小插曲，其中包括使用这些功能的加载数据的例子，找到的小插曲，help(library=TRAMPR)，然后滚动到页面底部的，或者类型：system.file("doc/TRAMPR_demo.pdf", package="TRAMPR")。
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。
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发表于 2012-10-1 11:43:25
