GeneSetCollection-methods(GSEABase)
GeneSetCollection-methods()所属R语言包：GSEABase
Methods to construct GeneSetCollection instances
方法构建GeneSetCollection实例
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Use GeneSetCollection to construct a collection of gene sets from GeneSet arguments, or a list of GeneSets.
使用GeneSetCollection从GeneSet参数，或GeneSet的名单构建基因组的集合。
用法----------Usage----------
GeneSetCollection(object, ..., idType, setType)
参数----------Arguments----------
参数：object
An argument determining how the gene set collection will be created, as described in the methods section.
确定如何将基因组集合创建，在方法部分所述的参数。
参数：...
Additional arugments for gene set collection construction, as described below.
为基因组收集建设的额外arugments，如下所述。
参数：idType
An argument of class GeneIdentifierType, used to indicate how the geneIds will be represented.
类的一个参数GeneIdentifierType，用来指示如何geneIds将代表。
参数：setType
An argument of class CollectionType, used to indicate how the collection is created.
类的一个参数CollectionType，用来指示如何创建集合。
方法----------Methods----------
Construct a gene set collection from one or more GeneSet arugments.
从一个或多个GeneSetarugments构建基因组集合。
Construct a gene set collection from a list of GeneSets.
构建基因组集合从GeneSet的名单。
Construct a gene set collection of CollectionType entities (e.g., pathways for KEGGCollection, protein families for PfamCollection) implied by the map found in annotation(idType). If setType is a CollectionIdType and length(ids(setType))>0, the gene set collection is filtered to contain only those sets implied by the ids.
构建基因组收集了CollectionType实体（例如，KEGGCollection，蛋白质家族的途径PfamCollection）annotation(idType)发现图的暗示。如果setType是一个CollectionIdType和length(ids(setType))>0，基因组集过滤，只包含那些由IDS暗示套。
Construct a gene set collection of CollectionType entities (e.g., pathways for KEGGCollection, protein families for PfamCollection) implied by the map found in annotation(idType). Use only those identifiers in object. If setType is a CollectionIdType and length(ids(setType))>0, the gene set collection is filtered to contain only those sets implied by the ids.
构建基因组收集了CollectionType实体（例如，KEGGCollection，蛋白质家族的途径PfamCollection）annotation(idType)发现图的暗示。使用object只有那些标识符。如果setType是一个CollectionIdType和length(ids(setType))>0，基因组集过滤，只包含那些由IDS暗示套。
Construct a gene set collection by mapping all values in object to PfamIds found in the PFAM map implied by idType.
所有值映射的构造基因组集合objectPfamIds图PFAM暗示在idType发现。
Construct a gene set collection by mapping all values in object to ipi_ids found in the PFAM map implied by idType.
所有值映射的构造基因组集合objectipi_ids图PFAM暗示在idType发现。
Construct a gene set collection by mapping all values in object to chromosome, strand, and position information found in the map implied by idType.
构建基因组集合，由映射object染色体，钢绞线，并发现在idType暗示的图中的位置信息值。
Construct a gene set collection using the annotation and featureNames of object to identify elements for CollectionType gene sets (e.g., pathways for KEGGCollection, protein families for PfamCollection) implied by object. The gene set collection contains only those AnnotationIdentifiers found in featureNames(object); if setType is a CollectionIdType and length(ids(setType))>0, the gene set collection is further filtered to contain only those sets implied by the ids.
构建一个基因组的集合，使用annotation和featureNamesobjectCollectionType基因集的识别元素（例如，KEGGCollection，蛋白质家族的途径 PfamCollection）object暗示。基因组的集合只包含那些AnnotationIdentifiers发现featureNames(object);setType1CollectionIdType和length(ids(setType))>0，基因组收集进一步过滤只包含由IDS暗示的套。
Construct a gene set collection using the annotation and featureNames of object to identify GO pathways implied by object. The map between featureNames and GO pathway identifiers is derived from the GO2PROBE table of the annotation package of object. The gene set collection contains only those AnnotationIdentifiers found in featureNames(object). The evidenceCode of GOCollection can be used to restrict the pathways seleted to those with matching evidence codes.
构建一个基因组的集合，使用annotation和featureNamesobject确定GO途径object暗示。图之间的featureNames和GO通路标识符GO2PROBEobject注解包表派生。基因组的集合包含只有那些AnnotationIdentifiersfeatureNames(object)。 evidenceCodeGOCollection可以用来限制相匹配的证据代码入围的途径。
Construct a gene set collection by mapping all values in featureNames(object) to PfamIds found in the PFAM map implied by idType=AnnotationIdentifer(annotation(object)).
所有值映射的构造基因组集合featureNames(object)PfamIds图PFAM暗示在idType=AnnotationIdentifer(annotation(object))发现。
Construct a gene set collection by mapping all values in featureNames(object) to ipi_id found in the PFAM map implied by idType=AnnotationIdentifer(annotation(object)).
所有值映射的构造基因组集合featureNames(object)ipi_id图PFAM暗示在idType=AnnotationIdentifer(annotation(object))发现。
Construct a gene set collection by mapping all values in featureNames(object) to chromosome, strand, and position information found in the CHRLOC map implied by idType=AnnotationIdentifer(annotation(object)).
映射featureNames(object)染色体，钢绞线，以及发现在CHRLOCidType=AnnotationIdentifer(annotation(object))暗示的图中的位置信息值，建构基因组集合。
Construct a gene set collection containing all GO pathways referenced in the GOALLFrame provided. Each gene set only those Identifiers found in GOALLFrame. The ontology of each GOALLFrame GO ID will be included in the gene Set of that GO ID .
构建一个基因组的集合，包含所有GOGOALLFrame提供参考途径。每个基因组只有那些IdentifiersGOALLFrame。 ontology每GOALLFrame去ID将包括在该GO ID设置的基因。
参见----------See Also----------
GeneSetCollection-class
GeneSetCollection级
举例----------Examples----------
gs1 <- GeneSet(setName="set1", setIdentifier="101")
gs2 <- GeneSet(setName="set2", setIdentifier="102")
## construct from indivdiual elements...[＃构造indivdiual元素...]
gsc <- GeneSetCollection(gs1, gs2)
## or from a list[＃或从列表]
gsc <- GeneSetCollection(list(gs1, gs2))
## set names must be unique[＃设置的名称必须是唯一]
try(GeneSetCollection(gs1, gs1))
data(sample.ExpressionSet)
gsc <- GeneSetCollection(sample.ExpressionSet[200:250],
setType = GOCollection())
## Not run: [＃无法运行：]
## from KEGG identifiers, for example[＃从KEGG标识符，例如]
library(KEGG.db)
lst <- head(as.list(KEGGEXTID2PATHID))
gsc <- GeneSetCollection(mapply(function(geneIds, keggId) {
GeneSet(geneIds, geneIdType=EntrezIdentifier(),
collectionType=KEGGCollection(keggId),
setName=keggId)
}, lst, names(lst)))
## End(Not run)[＃结束（不运行）]
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注：
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发表于 2012-2-25 21:17:00
