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

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OBOCollection-class(GSEABase)
OBOCollection-class()所属R语言包：GSEABase

                                        Class "OBOCollection"
                                         类“OBOCollection”

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

OBOCollection extends the GOCollection class, and is usually constructed from a file formated following the OBO file format. See CollectionType for general use of collections with gene sets.
OBOCollection延伸GOCollection类，通常是从一个格式化文件构建奥博文件格式。看到CollectionType集合的一般使用与基因组。


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

Objects are instantiated with calls to OBOCollection or getOBOCollection.
与调用OBOCollection或getOBOCollection的对象被实例化。


插槽----------Slots----------

OBOCollection extends GOCollection and OBOCollection has the following additional slots (these slots are NOT meant to be manipulated directly by the user):
OBOCollection延伸GOCollection和OBOCollection具有以下附加插槽（这些插槽并不意味着要由用户直接操纵）：




.stanza: A data.frame representing the stanzas present in an OBO file. Row names of the data frame are unique stanza identifiers. The value column contains the stanza name (e.g., "Term", i.e., the stanza name associated
.stanza：data.frame代表OBO的文件中的节。数据框的行名是唯一的节标识。 value列包含的节的名称（如“一词，即相关的节名




.subset A data.frame representing (optional) subsets defined in the collection. Subsets are defined in the header of an OBO file with a subsetdef tag. Row names of the data frame are the subsetdef names; the value column contains
.subsetAdata.frame代表（可选）亚群在集合中定义。 OBO的与subsetdef标记的文件头中定义子集。数据框的行名是subsetdef名;value列包含




.kv A data.frame representing key-value pairs in the OBO source file. The row names of the data frame correspond to lines in the OBO file. The stanza_id column indexes the row of .stanza describing the stanza in which the key-value pair occured. The remaining columns (key, value)
.kvAdata.frame代表奥博源文件中的键 - 值对。对应的数据框的行名行奥博文件中。 stanza_id列索引的行.stanza描述节中键 - 值对发生。其余列（key，value）


方法----------Methods----------

OBOCollection has the following methods, in addition to those inherited from GOCollection.
OBOCollection有以下几种方法，除了那些从GOCollection继承。

These methods list and select subsets of OBOCollection:
这些方法的列表，并选择OBOCollection子集：




subsets signature(object="OBOCollection", display="named"): return a character vector of subsets present in object. Valid values for display are "named" (a named character vector, with names equal to the names of the subsets and values the descriptions), "full" (a character vector of name and description, with each pair formated into a single entry as “name (description)”), "key" (subset names), or "value" (subset
亚群signature(object="OBOCollection", display="named")：返回一个子集的字符向量中存在object。有效display名为（一个命名的特征向量，等于子集和值的说明的名称的名称），全（的名称和描述的特征向量，每对值格式化成一个单一入口“的名称（描述）”），“关键”（子集名称），或“价值”（子集




[ signature(object="OBOCollection", i="character", j="missing", ...): return an OBOCollection by selecting just those subsets whose name matches the string(s) in i. This method calls the [,GOCollection method so, e.g., evidenceCode can be used to restricts which evidence codes the collection will
[signature(object="OBOCollection", i="character", j="missing", ...)：返回一个选择那些子集，其名称相匹配的字符串（S）OBOCollectioni。此方法调用[,GOCollection方法，所以，例如，evidenceCode可以用来限制证据代码集合

These methods coerce to and from OBOCollection:
这些方法强迫从OBOCollection：




as signature(object="OBOCollection", "graphNEL"): create a directed graph with nodes generated from ids(object) and edges from is_a relations of
signature(object="OBOCollection", "graphNEL")：创建带从ids(object)和is_a关系的边缘产生的节点的有向图




as signature(object="graphNEL", "OBOCollection"): create an OBOCollection with ids from the graph
signature(object="graphNEL", "OBOCollection")：与OBOCollection从图ids


作者（S）----------Author(s)----------


Martin Morgan <mtmorgan@fhcrc.org>



参考文献----------References----------



参见----------See Also----------

OBOCollection constructor;  CollectionType classes.
OBOCollection构造CollectionType类。


举例----------Examples----------


fl <- system.file("extdata", "goslim_plant.obo", package="GSEABase")
obo <- getOBOCollection(fl)
obo
subsets(obo)
obo["goslim_plant", evidenceCode="TAS"]
g <- as(obo["goslim_goa"], "graphNEL")
if (interactive() &amp;&amp; require("Rgraphviz")) {
    plot(g)
}

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


注：
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