R语言 KEGGgraph包 getKGMLurl()函数中文帮助文档(中英文对照)

loveR

getKGMLurl(KEGGgraph)
getKGMLurl()所属R语言包：KEGGgraph

                                         Get KGML file (url) with KEGG PATHWAY ID and (optional) organism
                                         获取KGML KEGG通路ID文件（URL）和（可选）生物体

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

The function simply returns the KGML file url given KEGG PATHWAY ID. If the KEGG PATHWAY ID contains no organism prefix, user can specify the 'organism' parameter. Otherwise the 'organism' option is ignored.
函数只是返回的KGML的的KEGG通路标识的文件的URL。如果KEGG通路ID包含没有有机体前缀，用户可以指定的“有机体”参数。否则，“有机体”选项被忽略。

retrieveKGML is a simple wrapper to getKGMLurl, which downloads the KGML file with download.file in utils package.
retrieveKGML是一个简单的包装，download.fileutils包KGML文件下载到getKGMLurl。


用法----------Usage----------


getKGMLurl(pathwayid, organism = "hsa")
retrieveKGML(pathwayid, organism, destfile,method="wget", ...)
kgmlNonmetabolicName2MetabolicName(destfile)
getCategoryIndepKGMLurl(pathwayid, organism="hsa", method="wget", ...)



参数----------Arguments----------

参数：pathwayid
KEGG PATHWAY ID, e.g. 'hsa00020'
KEGG通路ID，例如： “hsa00020”


参数：organism
three-alphabet organism code, if pathwayid contains the ocde this option is ignored
三个字母有机体代码，如果pathwayid包含的OCDE这个选项被忽略


参数：destfile
Destination file, to which the remote KGML file should be saved
目标文件，远程KGML文件应保存


参数：method
Method to be used for downloading files, passed to download.file function. Currently supports "internal", "wget" and "lynx"
要下载文件的方法，通过download.file功能。目前支持“内部”，“wget的”和“猞猁”


参数：...
Parameters passed to download.file
参数传递到download.file


Details

详情----------Details----------

The function getKGMLurl takes the pathway identifier (can be in the form of 'hsa00020' or with 'pathway' prefix, for example 'path:hsa00020'), and returns the url to download KGML file.
功能getKGMLurl通路标识符（可以在“hsa00020”的形式，或与“通路”的前缀，例如“路径：hsa00020），并返回的URL下载KGML文件。

The mapping between pathway identifier and pathway name can be found by KEGGPATHNAME2ID (or reversed mappings) in KEGG.db package. See vignette for example.
通路标识符和路径名之间的映射，可以发现在KEGG.db包由KEGGPATHNAME2ID（或反向的映射）。例如，看到小插曲。

retrieveKGML calls download.file to download the KGML file from KEGG FTP remotely.
retrieveKGML要求download.file远程下载从KEGG FTP KGML文件。

Since July 2011 the KGML is downloaded directly from the HTTP main page of each pathway, instead of from the FTP server. The FTP server is only open to subscribers. Commercial and other users should consider support the KEGG database by subscribing to the FTP service. See the references section below.
自2011年7月以来KGML每个通路的主要页面的HTTP直接下载，而不是从FTP服务器上。 FTP服务器是只开放给用户。商业和其他用户应考虑KEGG数据库订阅到FTP服务支持。请参阅下面的参考资料一节。


值----------Value----------

KGML File URL of the given pathway.
的途径KGML文件的URL。


注意----------Note----------

So far the function does not check the correctness of the 'organism' prefix, it is the responsibility of the user to garantee the right spelling.
到目前为止，该函数不检查有机体前缀的正确性，它是用户的的责任garantee正确的拼写。

For Windows users, it is necessary to download and install wget program (http://gnuwin32.sourceforge.net/packages/wget.htm) to use the wget method to download files. Sometimes it may be necessary to modify searching path to add GnuWin32 folder (where wget execution file is located) and re-install R to make wget work.
对于Windows用户，这是必要的下载和安装wget程序（http://gnuwin32.sourceforge.net/packages/wget.htm）使用wget方法下载文件。有时可能需要修改搜索路径增加而GnuWin32文件夹（其中wget执行文件所在），并重新安装Rwget工作。

Some user may experience difficulty of retrieving KGML files when the download method is set to "auto". In this case setting the method to "wget" may solve the problem (thanks to the report by Gilbert Feng).
的检索KGML文件下载方法设置为“自动”时，一些用户可能会遇到困难。在这种情况下“wget的设置方法可以解决的问题（以感谢吉尔伯特丰的报告）。

There were a period when the metabolic and non-metabolic pathways were saved separately in different directories, and KEGGgraph was able to handle them. kgmlNonmetabolicName2MetabolicName is used to translate non-metabolic pathway KGML URL to that of metabolic pathway. getCategoryIndepKGMLurl determines the correct URL to download by attempting both possibilities. They were mainly called internally. Now since the KGML file is to be downloaded in each pathway's main page instead from the FTp server, these functions are no more needed and will be removed in the next release.
有一个时期，代谢与非代谢途径分别保存在不同的目录KEGGgraph能够处理它们。 kgmlNonmetabolicName2MetabolicName使用翻译非代谢途径KGML的网址，代谢途径。 getCategoryIndepKGMLurl决定正确的URL下载试图通过这两种可能性。他们主要是在内部调用。现在以来的KGML的文件是要在每个通路的主网页，而不是从FTP服务器上下载，这些功能都没有更多的需要，将在下一版本中删除。


作者（S）----------Author(s)----------


Jitao David Zhang <a href="mailto:jitao_david.zhang@roche.com">mailto:jitao_david.zhang@roche.com</a>



参考文献----------References----------



举例----------Examples----------


getKGMLurl("hsa00020")
getKGMLurl("path:hsa00020")
getKGMLurl("00020",organism="hsa")
getKGMLurl(c("00460", "hsa:00461", "path:hsa00453", "path:00453"))

## NOT RUN[＃无法运行]
tmp <- tempfile()
retrieveKGML(pathwayid='00010', organism='cel', destfile=tmp, method="wget")

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。