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

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

                                        Class "GeneSetCollection"
                                         类“GeneSetCollection”

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

a GeneSetCollection is a collection of related GeneSets. The collection can mix and match different types of gene sets. Members of the collection are refered to by the setNames of each gene set.
GeneSetCollection是一个相关的GeneSet的集合。集合可以混合和匹配不同类型的基因组。集合的成员setName每个基因组的小号。


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

Construct a GeneSetCollection with a GeneSetCollection method, e.g., from a list of gene sets or with several gene sets provided as argument to the constructor. See examples below.
构建一个GeneSetCollection方法，例如GeneSetCollection，从基因组的列表作为参数的构造提供设置或几个基因。见下面的例子。


插槽----------Slots----------




.Data: Object of class "list", containing the
.Data：Object类的"list"，包含


延伸----------Extends----------

Class "list", from data part. Class "vector", by class "list", distance 2. Class "AssayData", by class "list", distance 2.
类"list"，从数据的一部分。类"vector"，由类“列表”，距离为2。类"AssayData"，由类“列表”，距离为2。


方法----------Methods----------

Gene set collection construction
基因组馆藏建设




GeneSetCollection See GeneSetCollection methods
GeneSetCollection见GeneSetCollection方法

Collection access (operations on lists, such as length, , lapply also work on GeneSetCollection).
集合的访问（如length，lapply还GeneSetCollection工作，名单上的操作）。




geneIds signature(object = "GeneSetCollection"): return a list, with each member a character vector of gene
geneIdssignature(object = "GeneSetCollection")：返回一个列表，每个成员的基因特征向量




geneIds<- signature(object="GeneSetCollection", value="list"): assign character vectors in value to
geneIds < - signature(object="GeneSetCollection", value="list")：value在分配特征向量




names signature(x = "GeneSetCollection"): return the
名signature(x = "GeneSetCollection")：返回

Logical and subsetting operations
逻辑和子集的操作

signature(x = "GeneSetCollection", y = "ANY"),
signature(x = "GeneSetCollection", y = "ANY")

signature(e1 = "GeneSetCollection", e2 = "ANY"), signautre(e1 = "GeneSet", e2 = "GeneSetCollection"), signautre(e1 = "character", e2 = "GeneSetCollection"), signature(e1 = "ANY", e2 = "GeneSetCollection"): calculate the logical 'or' (union) of all gene identifiers
signature(e1 = "GeneSetCollection", e2 = "ANY")，signautre(e1 = "GeneSet", e2 = "GeneSetCollection")，signautre(e1 = "character", e2 = "GeneSetCollection")，signature(e1 = "ANY", e2 = "GeneSetCollection")：计算逻辑“或”所有基因标识（工会）

signature(x = "GeneSetCollection", y = "ANY"),
signature(x = "GeneSetCollection", y = "ANY")

signature(e1 = "GeneSetCollection", e2 = "ANY"), signautre(e1 = "character", e2 = "GeneSetCollection"), signautre(e1 = "GeneSet", e2 = "GeneSetCollection"), signature(e1 = "ANY", e2 = "GeneSetCollection"): calculate the logical "and" (intersection) of all gene identifiers in a gene set or character vector, over all members of the gene
signature(e1 = "GeneSetCollection", e2 = "ANY")，signautre(e1 = "character", e2 = "GeneSetCollection")，signautre(e1 = "GeneSet", e2 = "GeneSetCollection")，signature(e1 = "ANY", e2 = "GeneSetCollection")：计算逻辑“和”基因在基因组或特征向量的所有标识符（路口），超过所有成员基因

signature(x = "GeneSetCollection", y = "ANY"): calculate the logical set difference betwen all gene sets in a collection and the gene identifiers of a gene set or character vector. A setdiff method must be available for
signature(x = "GeneSetCollection", y = "ANY")：悫集合中的所有基因组和基因组的基因标识或特征向量的计算逻辑的差集。必须提供一个setdiff方法

signature(x = "GeneSetCollection", i = "ANY", j = "ANY", value = "ANY"), signature(x = "GeneSetCollection", i = "ANY", j = "ANY", value = "GeneSet"), signature(x = "GeneSetCollection", i = "character", j = "ANY", value = "GeneSet"): assign new sets to existing set members. To add entirely new sets, use a GeneSetCollection constructor.
signature(x = "GeneSetCollection", i = "ANY", j = "ANY", value = "ANY")，signature(x = "GeneSetCollection", i = "ANY", j = "ANY", value = "GeneSet")，signature(x = "GeneSetCollection", i = "character", j = "ANY", value = "GeneSet")：分配新集现有的组的成员。添加全新套，使用GeneSetCollection构造。

signature(x = "GeneSetCollection", i = "logical"),  signature(x = "GeneSetCollection", i = "numeric"), signature(x = "GeneSetCollection", i = "character"): create a GeneSetCollection consisting of a subset of the current set. All indicies i must already be present in the set.
signature(x = "GeneSetCollection", i = "logical")，signature(x = "GeneSetCollection", i = "numeric")，signature(x = "GeneSetCollection", i = "character")：创建一个GeneSetCollection当前设置的一个子集组成。所有序号为i必须已经是目前集。

signature(x = "GeneSetCollection", i = "character"):  Select a single gene set from the collection. Methods for
signature(x = "GeneSetCollection", i = "character")：选择一个单一的基因，从集合。为方法

signature(x = "GeneSetCollection", i = "ANY", j = "ANY", value = "ANY"), signature(x = "GeneSetCollection", i = "numeric", j = "ANY", value = "GeneSet"), signature(x = "GeneSetCollection", i = "character", j = "ANY", value = "GeneSet"): Replace a gene set in the collecton with another.
signature(x = "GeneSetCollection", i = "ANY", j = "ANY", value = "ANY")，signature(x = "GeneSetCollection", i = "numeric", j = "ANY", value = "GeneSet")，signature(x = "GeneSetCollection", i = "character", j = "ANY", value = "GeneSet")：取代另一个collecton设置基因。

Additional useful methods.
更多有用的方法。

Objects created in previous versions of GSEABase may be incompatible with current object definitions. Usually this is singalled by an error suggesting that a slot is missing, and a recommnedation to use updateObject. Use updateObject to update a GeneSetCollection and all contained
对象以前版本GSEABase创建可能是不符合当前对象的定义。这通常是由一个错误表明一个插槽缺少singalled，和recommnedation使用updateObject。使用updateObjectGeneSetCollection和包含的所有更新

Convert genes from one GeneIdentifierType to another. See mapIdentifiers and specific methods in
转换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="GeneSetCollection"): provide a
显示signature(object="GeneSetCollection")：提供1


作者（S）----------Author(s)----------


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



参见----------See Also----------

GeneSet, GeneColorSet.
GeneSet，GeneColorSet。


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))

## 'names' are the setNames[＃名的setNames]
names(gsc)

## a collection of a single gene set[＃一个单一的基因组的集合]
gsc["set1"]
## a gene set[＃基因组]
gsc[["set1"]]

## set names must be unique[＃设置的名称必须是唯一]
try(GeneSetCollection(gs1, gs1))
try(gsc[c("set1", "set1")])

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


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