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

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

                                        Class "GeneSet"
                                         类“GeneSet”

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

A GeneSet contains a set of gene identifiers. Each gene set has a geneIdType, indicating how the gene identifiers should be interpreted (e.g., as Entrez identifiers), and a collectionType, indicating the origin of the gene set (perhaps including additional information about the set, as in the BroadCollection type).
一个GeneSet包含了一套基因标识。每个基因组有一个geneIdType，collectionType，表明基因组的起源（也许还包括有关设置的其他信息，表明基因标识应如何解释（例如，Entrez的标识符）， ，BroadCollection型）。

Conversion between identifiers, subsetting, and logical (set) operations can be performed. Relationships between genes and phenotype in a GeneSet can be summarized using coloring to create a GeneColorSet. A GeneSet can be exported to XML with toBroadXML.
可以进行识别，子集，逻辑（套）操作之间的转换。使用GeneSet创建一个coloring一个GeneColorSet表型和基因之间的关系可以概括。一个GeneSet可以导出到XMLtoBroadXML。


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

Construct a GeneSet with a GeneSet method (e.g., from a character vector of gene names, or an ExpressionSet), or from gene sets stored as XML (locally or on the internet; see getBroadSets)
构建与GeneSet方法（例如，从向量的基因名称的字符，或一个设置存储为XML（可在本地或在互联网上GeneSet），或从基因的ExpressionSet;看到getBroadSets）


插槽----------Slots----------




setName: Object of class "ScalarCharacter"
setName类"ScalarCharacter"：对象




setIdentifier: Object of class "ScalarCharacter" containing a (unique) identifier for the
setIdentifier类"ScalarCharacter"包含一个（唯一）标识符的对象为




geneIdType: Object of class "GeneIdentifierType" containing information about how the gene identifiers are encoded. See
geneIdType类"GeneIdentifierType"包含有关如何编码基因标识信息的对象。见




geneIds: Object of class "character" containing
geneIds：Object类的"character"包含




collectionType: Object of class "CollectionType" containing information about how the geneIds were collected, including perhaps additional information unique to the collection methodology. See CollectionType
collectionType：Object类的"CollectionType"含有的geneIds，包括独特的收集方法可能是额外的信息收集的信息。看到CollectionType




shortDescription: Object of class
shortDescription：对象类




longDescription: Object of class "ScalarCharacter" providing a longer description (e.g.,
longDescription类"ScalarCharacter"提供了一个较长的描述（如对象，




organism: Object of class "ScalarCharacter"
organism类"ScalarCharacter"：对象




pubMedIds: Object of class "character"
pubMedIds类"character"：对象




urls: Object of class "character" containing
urls：Object类的"character"包含




contributor: Object of class "character"
contributor类"character"：对象




version: Object of class "Versions" a version number, manually curated (i.e., by the contributor) to
version：Object类的"Versions"一个版本号，手动策划（即由的contributor）




creationDate: Object of class "character" containing the character string representation of the date on which
creationDate类"character"包含日期的字符串表示的对象


方法----------Methods----------

Gene set construction:
基因组结构：




GeneSet See GeneSet methods and
GeneSet见GeneSet方法

Slot access (e.g., setName) and retrieve (e.g., setName<-) :
插槽的访问（例如，setName）和检索（例如，setName<-）：




collectionType<- signature(object = "GeneSet", value = "CollectionType")
collectionType < - signature(object = "GeneSet", value = "CollectionType")




collectionType signature(object = "GeneSet")
collectionTypesignature(object = "GeneSet")




contributor<- signature(object = "GeneSet", value = "character")
贡献者< - signature(object = "GeneSet", value = "character")




contributor signature(object = "GeneSet")
的贡献者signature(object = "GeneSet")




creationDate<- signature(object = "GeneSet", value = "character")
creationDate < - signature(object = "GeneSet", value = "character")




creationDate signature(object = "GeneSet")
creationDatesignature(object = "GeneSet")




description<- signature(object = "GeneSet", value = "character")
说明< - signature(object = "GeneSet", value = "character")




description signature(object = "GeneSet")
说明signature(object = "GeneSet")




geneIds<- signature(object = "GeneSet", value = "character")
geneIds < - signature(object = "GeneSet", value = "character")




geneIds signature(object = "GeneSet")
geneIdssignature(object = "GeneSet")




longDescription<- signature(object = "GeneSet", value = "character")
longDescription < - signature(object = "GeneSet", value = "character")




longDescription signature(object = "GeneSet")
longDescriptionsignature(object = "GeneSet")




organism<- signature(object = "GeneSet", value = "character")
生物体< - signature(object = "GeneSet", value = "character")




organism signature(object = "GeneSet")
生物体signature(object = "GeneSet")




pubMedIds<- signature(object = "GeneSet", value = "character")
pubMedIds < - signature(object = "GeneSet", value = "character")




pubMedIds signature(object = "GeneSet")
pubMedIdssignature(object = "GeneSet")




setdiff signature(x = "GeneSet", y = "GeneSet")
setdiffsignature(x = "GeneSet", y = "GeneSet")




setIdentifier<- signature(object = "GeneSet", value = "character")
setIdentifier < - signature(object = "GeneSet", value = "character")




setIdentifier signature(object = "GeneSet")
setIdentifiersignature(object = "GeneSet")




setName<- signature(object = "GeneSet", value = "character")
的setName < - signature(object = "GeneSet", value = "character")




setName signature(object = "GeneSet")
的setNamesignature(object = "GeneSet")

signature(object = "GeneSet", verbose=FALSE, value = "character"), signature(object = "GeneSet", verbose=FALSE, value = "GeneIdentifierType"): These method attempt to coerce geneIds from the current type to the type named by value. Successful
signature(object = "GeneSet", verbose=FALSE, value = "character")，signature(object = "GeneSet", verbose=FALSE, value = "GeneIdentifierType")：这些方法尝试，强迫geneIds从目前的类型value命名类型。成功




geneIdType signature(object = "GeneSet")
geneIdTypesignature(object = "GeneSet")




setVersion<- signature(object = "GeneSet", value = "Versions")
setVersion < - signature(object = "GeneSet", value = "Versions")




setVersion signature(object = "GeneSet")
setVersionsignature(object = "GeneSet")




urls<- signature(object = "GeneSet", value = "character")
网址< - signature(object = "GeneSet", value = "character")




urls signature(object = "GeneSet")
网址signature(object = "GeneSet")

Logical and subsetting operations:
逻辑和子集的操作：




union signature(x = "GeneSet", y = "GeneSet"): ...
工会signature(x = "GeneSet", y = "GeneSet")...




| signature(e1 = "GeneSet", e2 = "GeneSet"): calculate the logical "or" (union) of two gene sets. The sets must contain elements of
|signature(e1 = "GeneSet", e2 = "GeneSet")：计算逻辑“或”两个基因组（联盟）。集必须包含的元素

signature(e1 = "GeneSet", e2 = "character"), signature(e1 = "character", e2 = "GeneSet"): calculate the logical "or" (union) of a gene set and a character vector,
signature(e1 = "GeneSet", e2 = "character")，signature(e1 = "character", e2 = "GeneSet")：计算逻辑“或”（联盟）的基因组和特征向量，




intersect signature(x = "GeneSet", y = "GeneSet"):
相交signature(x = "GeneSet", y = "GeneSet")：




&amp; signature(e1 = "GeneSet", e2 = "GeneSet"): calculate
＆signature(e1 = "GeneSet", e2 = "GeneSet")：计算

signature(e1 = "GeneSet", e2 = "character"), signature(e1 = "character", e2 = "GeneSet"): calculate the logical "and" (intersection) of a gene set and a character vector, creating a new gene set containing only those
signature(e1 = "GeneSet", e2 = "character")，signature(e1 = "character", e2 = "GeneSet")：计算逻辑“和”基因组和特征向量（路口），创建一个新的基因组只包含那些

signature(x = "GeneSet", y = "GeneSet"), signature(x = "GeneSet", y = "character"), signature(x = "character", y = "GeneSet"): calculate the logical set difference betwen two gene sets, or
signature(x = "GeneSet", y = "GeneSet")，signature(x = "GeneSet", y = "character")，signature(x = "character", y = "GeneSet")：介乎两个基因组计算逻辑的差集，或

signature(x = "GeneSet", i="character") signature(x = "GeneSet", i="numeric"): subset the gene set by index (i="numeric") or value (i="character"). Genes
signature(x = "GeneSet", i="character")signature(x = "GeneSet", i="numeric")：指数（i="numeric"）或值（i="character"）基因的子集。基因

signature(x = "ExpressionSet", i = "GeneSet"): subset the expression set, using genes in the gene set to select features. Genes in the gene set are coerced to appropriate annotation type if necessary (by consulting the annotation slot of the
signature(x = "ExpressionSet", i = "GeneSet")：子集表达式设置，使用设置选择功能基因的基因。在基因组的基因被裹挟适当的注释类型，如果必要（由咨询annotation插槽




[[ signature(x = "GeneSet"): select a single gene from
[signature(x = "GeneSet")：选择一个单一的基因




\$ signature(x = "GeneSet"): select a single gene from
\ $signature(x = "GeneSet")：选择一个单一的基因

Useful additional methods include:
有用的其他方法包括：




GeneColorSet signature(type = "GeneSet"): create a 'color' gene set from a GeneSet, containing information about phenotype. This method has a required argument phenotype, a character string describing the phenotype for
GeneColorSetsignature(type = "GeneSet")：创建一个“颜色”的基因GeneSet含有大约型的信息，设置。这种方法有一个必要的参数phenotype，字符串描述型




mapIdentifiers Use the code in the examples to list available methods. These convert genes from one GeneIdentifierType to another. See mapIdentifiers and specific methods in
的mapIdentifiers使用示例中的代码来列出可用的方法。这些转换从一个GeneIdentifierType到另一个基因。 mapIdentifiers和具体方法




incidence Summarize shared membership in genes across gene
发病总结共享成员的基因在整个基因




toGmt Export to 'GMT' format file. See toGmt.
toGmt出口到“时间”格式的文件。看到toGmt。




show signature(object = "GeneSet"): display a short
显示signature(object = "GeneSet")：显示一个短




details signature(object = "GeneSet"): display
细节signature(object = "GeneSet")：显示




initialize signature(.Object = "GeneSet"): Used
初始化signature(.Object = "GeneSet")：


作者（S）----------Author(s)----------


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



参见----------See Also----------

GeneColorSet CollectionType GeneIdentifierType
GeneColorSetCollectionTypeGeneIdentifierType


举例----------Examples----------


## Empty gene set[＃空的基因组]
GeneSet()
## Gene set from ExpressionSet[＃ExpressionSet基因组]
data(sample.ExpressionSet)
gs1 <- GeneSet(sample.ExpressionSet[100:109])
## GeneSet from Broad XML; 'fl' could be a url[从广泛的XML＃GeneSet;FL可能是一个网址]
fl <- system.file("extdata", "Broad.xml", package="GSEABase")
gs2 &lt;- getBroadSets(fl)[[1]] # actually, a list of two gene sets[实际上，这两个基因的集列表]
## GeneSet from list of geneIds[＃GeneSet geneIds名单]
geneIds &lt;- geneIds(gs2) # any character vector would do[会做任何特征向量]
gs3 <- GeneSet(geneIds=geneIds)
## unspecified set type, so...[＃未指定设置的类型，所以...]
is(geneIdType(gs3), "NullIdentifier") == TRUE
## update set type to match encoding of identifiers[＃更新设置的类型相匹配的标识符的编码]
geneIdType(gs2)
geneIdType(gs3) <- SymbolIdentifier()

## Convert between set types; this consults the 'annotation'[＃集类型之间的转换;咨询“注释”]
## information encoded in the 'AnnotationIdentifier' set type and the[＃“AnnotationIdentifier集类型的信息编码和]
## corresponding annotation package.[＃相应的注释包。]
## Not run: [＃无法运行：]
gs4 <- gs1
geneIdType(gs4) <- EntrezIdentifier()

## End(Not run)[＃结束（不运行）]

## logical (set) operations[＃逻辑操作（套）]
gs5 <- GeneSet(sample.ExpressionSet[100:109], setName="subset1")
gs6 <- GeneSet(sample.ExpressionSet[105:114], setName="subset2")
## intersection: 5 'genes'; note the set name '(subset1 &amp; subset2)'[＃路口：5基因;注意集名称“（subset1 subset2）]
gs5 &amp; gs6
## union: 15 'genes'; note the set name[＃工会：15基因;注意集名称]
gs5 | gs6
## an identity[＃身份]
gs7 <- gs5 | gs6
gs8 <- setdiff(gs5, gs6) | (gs5 &amp; gs6) | setdiff(gs6, gs5)
identical(geneIds(gs7), geneIds(gs8))
identical(gs7, gs8) == FALSE # gs7 and gs8 setNames differ[GS7和GS8 setNames不同]

## output[＃输出]
tmp <- tempfile()
toBroadXML(gs2, tmp)
noquote(readLines(tmp))
## must be BroadCollection() collectionType [＃必须BroadCollection（）collectionType，]
try(toBroadXML(gs1))
gs9 <- gs1
collectionType(gs9) <- BroadCollection()
toBroadXML(gs9, tmp)
unlink(tmp)
toBroadXML(gs9) # no connection --&gt; character vector[没有连接 - >特征向量]
## list of geneIds --&gt; vector of Broad GENESET XML[＃的geneIds列表 - >广泛GENESET XML的矢量]
gs10 &lt;- getBroadSets(fl) # two sets[两套]
entries <- sapply(gs10, function(x) toBroadXML(x))

## list mapIdentifiers available for GeneSet[＃列出mapIdentifiers为GeneSet]
showMethods("mapIdentifiers", classes="GeneSet", inherit=FALSE)

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


注：
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