CollectionType-class(GSEABase)
CollectionType-class()所属R语言包：GSEABase
Class "CollectionType"
类“CollectionType”
译者：生物统计家园网 机器人LoveR
描述----------Description----------
These classes provides a way to tag the origin of a GeneSet. Collection types can be used in manipulating (e.g., selecting) sets, and can contain information specific to particular sets (e.g., category and subcategory classifications of BroadCollection.)
这些类提供的方法标记GeneSet的起源。集合类型可以用于操纵（如选择）套，并可以包含具体到特定的集信息（例如，category和subcategoryBroadCollection的分类。）
类的对象----------Objects from the Class----------
The following classes can tag gene sets; GO, KEGG, Chr, Chrloc, OMIM, and PMID collections can be derived from chip or organism "annotation" packages.
下面的类可以标记基因套;GO, KEGG, Chr, Chrloc, OMIM, and PMID集合可以从芯片或生物体的注解包的。
NullCollection No formal collection information available.
NullCollection没有正式收集信息。
BroadCollection Derived from, or destined to be, Broad XML. Usually created and written getBroadSets,
BroadCollection来自或注定要成为广泛的XML。通常创建和书面getBroadSets，
ComputedCollection A computationally created collection, e.g.,
ComputedCollection计算创建的集合，例如，
ExpressionSetCollection Derived from ExpressionSet. Usually created during a call to GeneSet or
从ExpressionSetExpressionSetCollection派生。通常在创建过程中调用一个GeneSet
GOCollection Collection derived using Gene Ontology (GO)
GOCollection收集而得使用基因本体论（好）
OBOCollection Collection derived from GOCollection, specifically from files described by the OBO file format. See
从GOCollection派生OBOCollection收集，特别是从由OBO文件格式的描述文件。见
KEGGCollection Collection derived using KEGG terms.
KEGGCollection收集而得使用KEGG条款。
ChrCollection Collection derived using chromsome locations
ChrCollection收集的染色体位置
ChrlocCollection Collection derived using chromosome starting
ChrlocCollection收集而得染色体开始
MapCollection Collection derived from cytogenic bands.
MapCollection收集来自单元遗传学带。
OMIMCollection Collection derived from identifiers in the
在标识符派生的OMIMCollection收集
PMIDCollection Collection derived from PMID identifiers.
关键词标识符PMIDCollection收集来自。
PfamCollection Collection derived from Pfam identifiers.
PfamCollection收集派生从PFAM标识。
PrositeCollection Collection derived from Prosite identifiers.
PrositeCollection收集来自PROSITE标识符。
Objects are instantiated with calls to CollectionType constructors, with slot names as possible arguments.
对象实例调用CollectionType构造，与尽可能参数插槽名称。
插槽----------Slots----------
CollectionType classes (Null, ComputedCollection, ExpressionSet) have the slot:
CollectionType类（Null, ComputedCollection, ExpressionSet）插槽：
type: Object of class "ScalarCharacter" containing the character string representation of this
type：对象类的"ScalarCharacter"含此字符的字符串表示形式
CollectionIdType classes (KEGG, OMIM, PMID, Chr, Chrloc, Map, GO) extend the CollectionType and have the additional slot:
CollectionIdType类（KEGG, OMIM, PMID, Chr, Chrloc, Map, GO）延长CollectionType并有额外的插槽：
ids: Object of class "character" containing a vector of character string representations of corresponding
ids：类对象"character"包含一个相应的字符串表示的向量
GOCollection extends CollectionIdType and has the additional slot:
GOCollection延伸CollectionIdType并有额外的插槽：
evidenceCode: Object of class "character",
evidenceCode：Object类的"character"，
ontology Object of class "character" vector of GO
本体对象"character"类好向量
The values of evidenceCode are
evidenceCode值
EXP Inferred from Experiment
从实验推断的进出口
IDA Inferred from Direct Assay
国际开发协会从直接分析推断
IPI Inferred from Physical Interaction
工业生产指数从物理相互作用推断
IMP Inferred from Mutant Phenotype
进出口推断从突变体
IGI Inferred from Genetic Interaction
IGI证书从遗传相互作用推断
IEP Inferred from Expression Pattern
IEP的推断从表达模式
ISS Inferred from Sequence or Structural Similarity
国际空间站从序列或结构相似性推断
ISO Inferred from Sequence Orthology
ISO推断从序列直向
ISA Inferred from Sequence Alignment
赛从序列比对推断
ISM Inferred from Sequence Model
推断的ISM从序列模型
IGC Inferred from Genomic Context
IGC的推断，从基因组上下文
RCA inferred from Reviewed Computational Analysis
从计算分析评价的RCA推断
TAS Traceable Author Statement
评审制溯源作者声明
NAS Non-traceable Author Statement
NAS的非溯源作者声明
IC Inferred by Curator
集成电路由馆长推断
ND No biological Data available
ND折价没有可用的生物数据
IEA Inferred from Electronic Annotation
国际能源署推断从电子注释
OBOCollection extends GOCollection; see OBOCollection.
OBOCollection延伸GOCollection见OBOCollection。
BroadCollection has slots:
BroadCollection插槽：
category: Object of class "ScalarCharacter"
category类"ScalarCharacter"：对象
subCategory: Object of class "ScalarCharacter"
subCategory类"ScalarCharacter"：对象
方法----------Methods----------
CollectionType classes have methods:
CollectionType类的方法：
collectionType<- signature(object = "GeneSet", value =
collectionType < - 的<code>签名（对象=“GeneSet”，值=
collectionType signature(object = "CollectionType"):
collectionTypesignature(object = "CollectionType")：
|, &, intersect, union, setdiff signature(e1="CollectionType", e2="CollectionType"): return e1 when class(e1) and
|，＆，相交，工会，setdiffsignature(e1="CollectionType", e2="CollectionType")：返回e1时class(e1)“
show signature(object = "CollectionType"): display the
显示signature(object = "CollectionType")：显示
CollectionIdType classes inherit CollectionType methods, and have in addition:
CollectionIdType类继承CollectionType方法，除了有：
ids signature(object="CollectionIdType"): Retrieve the
IDSsignature(object="CollectionIdType")：检索
[ signature(object="CollectionIdType", i="missing", j="missing", ..., ids=ids(object)): return a subset of
[signature(object="CollectionIdType", i="missing", j="missing", ..., ids=ids(object))：返回一个子集
signature(e1="CollectionIdType", e2="CollectionIdType"):
signature(e1="CollectionIdType", e2="CollectionIdType")：
GOCollection inherits CollectionIdType methods, and has in addition:
GOCollection继承CollectionIdType方法，除了有：
evidenceCode Retrieve the evidence codes of the GO
evidenceCode找回好证据代码
ontology Retrieve the ontology terms of the GO
本体检索的GO本体条款
[ signature(object="CollectionIdType", i="missing", j="missing", ..., evidenceCode=evidenceCode(object), ontology=ontology(object)): return a subset of object containing only evidence and ontology codes in evidenceCode, ontology. This method passes
[signature(object="CollectionIdType", i="missing", j="missing", ..., evidenceCode=evidenceCode(object), ontology=ontology(object))：返回一个object只包含的证据和evidenceCode，ontology本体码的子集。该方法通过
BroadCollection has methods:
BroadCollection方法有：
bcCategory Retrieve the category of the Broad
bcCategory找回了广大category
bcSubCategory Retrieve the sub-category of the Broad
bcSubCategory找回了广大的子类
作者（S）----------Author(s)----------
Martin Morgan <mtmorgan@fhcrc.org>
参见----------See Also----------
CollectionType consturctors; getBroadSets for importing collections from the Broad (and sources).
CollectionType的consturctors;getBroadSets进口从广义（源）的集合。
举例----------Examples----------
names(getClass("CollectionType")@subclasses)
## Create a CollectionType and ask for its type[＃创建一个CollectionType，并要求其类型]
collectionType(ExpressionSetCollection())
## Read two GeneSets from a Broad XML file into a list, verify that[＃从广泛的XML文件读取到列表GeneSets，验证]
## they are both BroadCollection's. Category / subcategory information[＃他们都是BroadCollection的。类别/子类别的信息]
## is unique to Broad collections.[＃是唯一广泛收藏。]
fl <- system.file("extdata", "Broad.xml", package="GSEABase")
sets <- getBroadSets(fl)
sapply(sets, collectionType)
## ExpressionSets are tagged with ExpressionSetCollection; there is no[＃ExpressionSets的标签ExpressionSetCollection没有]
## 'category' information.[＃“类的信息。]
data(sample.ExpressionSet)
gs <- GeneSet(sample.ExpressionSet[100:109],
setName="sample.GeneSet", setIdentifier="123")
collectionType(gs)
## GOCollections are created by reference to GO terms and evidenceCodes[被创建＃GOCollections参考去条款和evidenceCodes，，]
GOCollection("GO:0005488")
## requires library(GO); EntrezIdentifers automatically created[＃需要库（好）; EntrezIdentifers自动创建]
## Not run: [＃无法运行：]
GeneSet(GOCollection(c("GO:0005488", "GO:0019825"),
evidenceCode="IDA"))
## End(Not run)[＃结束（不运行）]
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 21:15:38
