R语言 AffyCompatible包 NetAffxResource-class()函数中文帮助文档(中英文对照)

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NetAffxResource-class(AffyCompatible)
NetAffxResource-class()所属R语言包：AffyCompatible

                                        Manage NetAffx annotations
                                         管理NetAffx注解

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

This class is for accessing and retrieving NetAffx annotation files for Affymetrix chips. It requires that the user has established an account with Affymetrix. Detailed usage is described in
这个类是Affymetrix公司芯片NetAffx批注文件的访问和检索。它需要用户已与Affymetrix公司建立了一个帐户。详细的使用说明


类的对象----------Objects from the Class----------

Objects are created by calls of the form NetAffxResource(user="user@research.org", password="terces"), as illustrated below and in the 'Annotations with NetAffx vignette.
创建对象的形式NetAffxResource(user="user@research.org", password="terces")检测，下面的说明，并在“批注NetAffx暗角。


插槽----------Slots----------




user: Object of class "character" containing the full user name (typically an email address) obtained when the
user：Object类的"character"包含完整的用户名（通常是电子邮件地址）时，得到




password: Object of class "character" containing the password associated with the Affymetrix user name. The password is entered and stored in plain text, and should
password：Object类的"character"含有与Affymetrix公司的用户名关联的密码。输入密码和存储在纯文本中，应该




affxLicence: Object of class "character" containing the licence, obtained from Affymetrix, for retrieving NetAffx annotations. The licence is usually software specific (e.g., for the AffyCompatible package of Bioconductor). Users will
affxLicence：Object类的"character"许可证，获得由Affymetrix公司，包含检索NetAffx注解。牌照通常是特定软件（例如，对于的Bioconductor AffyCompatible的包）。用户会




directory: Object of class "character", containing the local directory path where the NetAffx data base
directory类"character"，包含本地目录路径的地方NetAffx数据的基础上：对象




annotationsFile: Object of class "character" containing the file name of the NetAffx data base. Users will not
annotationsFile：Object类的"character"包含的NetAffx数据的基础上的文件名。用户将不会




affxUrl: Object of class "character" containing the URL used to download the NetAffx annotations file. Users will
affxUrl：Object类的"character"包含用于下载的NetAffx的注释文件的URL。用户会


延伸----------Extends----------

Class "NetAffxCompatibility", directly. Class "AffyCompatible", by class "NetAffxCompatibility", distance 2.
类"NetAffxCompatibility"，直接。类"AffyCompatible"，由类“NetAffxCompatibility”，距离为2。


方法----------Methods----------

signature(x = "NetAffxResource", i = "numeric", j = "missing")
signature(x = "NetAffxResource", i = "numeric", j = "missing")

signature(x = "NetAffxResource", i = "character", j = "missing"): Retrieve an object representing all NetAffx annotations available for an array. The argument i may be a numeric index or character string corresponding to an array name returned by names(x).
signature(x = "NetAffxResource", i = "character", j = "missing")：检索对象代表所有可用于数组NetAffx注释。参数i可能是一个数字索引或字符串names(x)返回一个数组名对应。

signature(x = "NetAffxResource", i = "numeric", j = "numeric")
signature(x = "NetAffxResource", i = "numeric", j = "numeric")

signature(x = "NetAffxResource", i = "character", j = "numeric")
signature(x = "NetAffxResource", i = "character", j = "numeric")

signature(x = "NetAffxResource", i = "numeric", j = "character")
signature(x = "NetAffxResource", i = "numeric", j = "character")

signature(x = "NetAffxResource", i = "character", j = "character"): Retrieve an object representing a specific annotation for an array. The argument i may be a numeric index or character string corresponding to an array name returned by names(x). The argument i may be a numeric index or character string corresonding to an annotation returned by description(x[[i]]).
signature(x = "NetAffxResource", i = "character", j = "character")：检索对象代表一个数组的具体注释。参数i可能是一个数字索引或字符串names(x)返回一个数组名对应。参数i可能是一个数字索引或字符的字符串corresondingdescription(x[[i]])返回一个注解。




affxLicence signature(x = "NetAffxResource"):  the character string representation of the licence used to access
affxLicencesignature(x = "NetAffxResource")：牌照字符的字符串表示形式用于访问




affxUrl signature(x = "NetAffxResource"): the
affxUrlsignature(x = "NetAffxResource")：




annotationsFile signature(x = "NetAffxResource"): the file name of NetAffx data base, as stored on the local disk of the
annotationsFilesignature(x = "NetAffxResource")：NetAffx数据的基础上的文件名，存储在本地磁盘




directory signature(x = "NetAffxResource"): the directory in wich the NetAffx data base and annotation files are
目录signature(x = "NetAffxResource")：wich的NetAffx数据的基础上和注释文件目录




names signature(x = "NetAffxResource"): the names of
名称signature(x = "NetAffxResource")：名称




password signature(x = "NetAffxResource"): The password associated with the user name obtained when the user registered with Affymetrix. The password is entered and stored as
密码signature(x = "NetAffxResource")：与Affymetrix用户注册时获得的用户名密码。输入密码和存储

signature(netAffxResource = "NetAffxResource", array = "numeric", annotation = "numeric", ...)
signature(netAffxResource = "NetAffxResource", array = "numeric", annotation = "numeric", ...)

signature(netAffxResource = "NetAffxResource", array = "numeric", annotation = "character", ...)
signature(netAffxResource = "NetAffxResource", array = "numeric", annotation = "character", ...)

signature(netAffxResource = "NetAffxResource", array = "character", annotation = "numeric", ...)
signature(netAffxResource = "NetAffxResource", array = "character", annotation = "numeric", ...)

signature(netAffxResource = "NetAffxResource", array = "character", annotation = "character", ...)
signature(netAffxResource = "NetAffxResource", array = "character", annotation = "character", ...)

signature(netAffxResource = "NetAffxResource", array = "missing", annotation = "AffxAnnotation", ...):  Read a specific anntotation file as an R object. for the first four methods, array, if present, indexes or names the array while annotation indexes or names the annotation. All methods also accept content = "logical" to indicate whether the content of the file should be returned if possible (content=TRUE, default) or only the path to the local file (content=FALSE) and update = "logical" indicating whether the file should be read from disk if available (update=FALSE, default) or retrieved from the NetAffx web site (update=TRUE). readAnnotation parses CSV, Tabular, and PSI files to data frames, and reads FASTA files to a list of description / sequence pairs (see Biostrings::readFASTA).
signature(netAffxResource = "NetAffxResource", array = "missing", annotation = "AffxAnnotation", ...)：阅读作为一个R对象的的具体anntotation文件。前四种方法，array目前，索引或名称，数组，如果同时annotation索引或名称注释。所有的方法也接受content = "logical"来指示该文件的内容是否应返回如果可能的话，（content=TRUE，默认情况下），或只到本地文件的路径（content=FALSE）<X >指示文件是否应该从磁盘读取，如果有（update = "logical"，默认）或检索从NetAffx网站（update=FALSE）。 update=TRUE解析CSV，表格和PSI数据框的文件，并读取readAnnotation文件描述/序列对（见FASTA）。

The ... argument is passed to corresponding read functions. CSV files are parsed using read.csv(conn, ...), Tabular files with read.delim(conn, ...), PSI files with read.delim(conn, header=FALSE, skip=1, sep="\t", ...), and FASTA with readFASTA(conn, ...).
...参数被传递到相应的读取功能。 CSV文件进行解析，用read.csv(conn, ...)，read.delim(conn, ...)，与readFASTA FASTA格式（CONN）PSI文件read.delim(conn, header=FALSE, skip=1, sep="\t", ...)，表格文件。




show signature(object = "NetAffxResource"): compactly
显示signature(object = "NetAffxResource")：紧




user signature(x = "NetAffxResource"): The user name (typcially email address) obtained when the user registers with
用户signature(x = "NetAffxResource")：用户名（typcially电子邮件地址）用户注册时获得


作者（S）----------Author(s)----------


Martin Morgan &lt;mtmorgan@fhcrc.org&gt;



参见----------See Also----------

Vignette "Annotations with NetAffx". Affymetrix user login site https://www.affymetrix.com/site/login/login.affx.
暗角“NetAffx的注解”。 Affymetrix公司的用户登录网站https://www.affymetrix.com/site/login/login.affx的。

.Rprofile for ways to automatically set variables (such as password, and directory) for each session.
.Rprofile自动设置变量（如password和directory）每届会议的方式。


举例----------Examples----------



## password must be obtained by the user[＃必须获得用户密码]
rsrc <- NetAffxResource(user="mtmorgan@fhcrc.org", password=password)
head(names(rsrc))
affxDescription(rsrc[["Bovine"]])
## paradigm to display all elements of 'annotation'[＃范例显示“注释”的所有元素]
sapply(affxAnnotation(rsrc[["Bovine"]]), force)
## obtain and read a single annotation[＃获取和读取一个注解]
anno <- rsrc[["Porcine", "BLASTP annotations, CSV Format"]]
df <- readAnnotation(rsrc, annotation=anno)

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注：
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