GeneColorSet-class(GSEABase)
GeneColorSet-class()所属R语言包：GSEABase
Class "GeneColorSet"
类“GeneColorSet”
译者：生物统计家园网 机器人LoveR
描述----------Description----------
A GeneColorSet extends GeneSet to allow genes to be 'colored'. Coloring means that for a particular phenotype, each gene has a color (e.g., expression levels "up", "down", or "unchanged") and a phenotypic consequence (e.g., the phenotype is "enhanced" or "reduced").
一个GeneColorSet延伸GeneSet允许基因是色。着色是指一个特定的表型，每个基因都有一种颜色（例如，表达水平的“上升”，“下降”或“不变”）和表型的后果（例如，表型是“强化”或“ ;减少“）。
All operations on a GeneSet can be applied to a GeneColorSet; coloring can also be accessed.
可应用于所有操作GeneSet到GeneColorSet;着色也可以访问。
类的对象----------Objects from the Class----------
Construct a GeneColorSet with a GeneColorSet method. These methods are identical to those for GeneSet, except they require an additional phenotype argument to specify the phenotype to which the genetic and phenotypic coloring apply. A GeneColorSet can be constructed from a GeneSet with GeneColorSet(<GeneSet>, phenotype="<phenotype>").
构建GeneColorSet方法与GeneColorSet。这些方法是相同的那些GeneSet，除非他们需要一个额外的phenotype参数指定的表型的遗传和表型的着色。可以构造一个GeneColorSet的GeneSet与GeneColorSet(<GeneSet>, phenotype="<phenotype>").
插槽----------Slots----------
A GeneColorSet inherits all slots from GeneSet, and gains the following slots:
一个GeneColorSet继承GeneSet，并获得以下插槽所有插槽：
phenotype: Object of class "ScalarCharacter"
phenotype类"ScalarCharacter"：对象
geneColor: Object of class "factor" describing the coloring of each gene in the set. The lengths of
geneColor类"factor"描述的每个基因组中的着色对象。长度
phenotypeColor: Object of class "factor" describing the phenotypic coloring of each gene in the set. The
phenotypeColor类"factor"描述集合中的每一个基因的表型着色的对象。 “
延伸----------Extends----------
Class "GeneSet", directly.
类"GeneSet"，直接。
方法----------Methods----------
Methods unique to GeneColorSet include:
GeneColorSet独特的方法包括：
coloring signature(object = "GeneColorSet"): retrieve coloring as a data.frame. The row names of the data frame are the gene names; the columns are geneColor and
着色signature(object = "GeneColorSet")：检索data.frame着色。数据框的行名是基因名称列geneColor“
coloring<- signature(object = "GeneColorSet", value = "data.frame"): use a data frame to assign coloring information. The data.frame must have the same number of rows as the GeneColorSet has genes (though see the examples below for flexible ways to alter coloring of a subset of genes). Row names of the data.frame correspond to gene names. The data frame has two columns, named geneColor and phenotypeColor. These must be of class factor.
着色< - signature(object = "GeneColorSet", value = "data.frame")使用data frame分配着色的信息。 data.frame必须有相同的行数GeneColorSet有基因（虽然下面的例子中看到灵活的方式来改变基因的一个子集的着色）。 data.frame行名称对应基因名称。数据框有两列，名为geneColor和phenotypeColor。这些必须是类factor。
A typical use of coloring<- is to simultaneous extract, subset, and reassign the current coloring, e.g., coloring(<GeneColorSet>)[1:5,"geneColor"] <- "up"; see the
一个典型的使用coloring<-是同步提取，子集，并重新分配，目前的着色，例如，coloring(<GeneColorSet>)[1:5,"geneColor"] <- "up";见
geneColor<- signature(object = "GeneColorSet", value =
geneColor < - 的<code>签名（对象=“GeneColorSet”，价值
geneColor signature(object = "GeneColorSet"): retrieve
geneColorsignature(object = "GeneColorSet")：检索
phenotypeColor<- signature(object = "GeneColorSet",
phenotypeColor < - 的<code>签名（对象=的“GeneColorSet”，
phenotypeColor signature(object = "GeneColorSet"):
phenotypeColorsignature(object = "GeneColorSet")：
phenotype<- signature(object = "GeneColorSet", value = "character"): assign the phenotype from a single-element
型< - signature(object = "GeneColorSet", value = "character")：指定的表型，从单一元素
phenotype signature(object = "GeneColorSet"): retrieve
型signature(object = "GeneColorSet")：检索
GeneColorSet inherits all methods from class GeneSet. Methods with different behavior include
GeneColorSet类GeneSet继承的所有方法。具有不同的行为的方法包括：
signature(x = "GeneSet", i="character") signature(x = "GeneSet", i="numeric"): subset the gene set by index (i="numeric") or gene value (i="character"). Genes are re-ordered as required. geneColor and phenotypeColor are
signature(x = "GeneSet", i="character")signature(x = "GeneSet", i="numeric")：指数（i="numeric"）或基因值（i="character"）基因的子集。基因重新排序的要求。 geneColor和phenotypeColor是
[[ signature(x = "GeneSet"): select a single gene from the gene set, returning a named character vector of gene,
[signature(x = "GeneSet")：选择一个单一的基因，从基因组返回的<code>基因的命名的特征向量，
\$ signature(x = "GeneSet"): select a single gene from the gene set, returning a named character vector of gene, geneColor, phenotypeColor. Provides partial matching into the
\ $signature(x = "GeneSet")：选择单一的基因，从基因组返回gene, geneColor, phenotypeColor的命名字符向量。将提供部分匹配
mapIdentifiers signature(x="GeneColorSet", to="*", from="*"): checks that gene- and phenotype colors are consistent for mapped identifiers, e.g., that two AnnotationIdentifiers mapping
mapIdentifierssignature(x="GeneColorSet", to="*", from="*")：检查映射标识符，例如，基因表型的颜色是一致的，这两个AnnotationIdentifiers映射
Logical (set) operations &, |, setdiff warn if the phenotype geneColor, or phenotypeColor differs between sets; this implies coercion of factor levels, and the consequences should be carefully considered.
逻辑（套）操作&, |, setdiff当phenotypegeneColor或phenotypeColor不同组之间，这意味着强迫因子水平，应慎重考虑后果。
作者（S）----------Author(s)----------
Martin Morgan <mtmorgan@fhcrc.org>
参见----------See Also----------
GeneSet.
GeneSet。
举例----------Examples----------
## Create a GeneColorSet from an ExpressionSet[＃创建一个从ExpressionSet GeneColorSet]
data(sample.ExpressionSet)
gcs1 <- GeneColorSet(sample.ExpressionSet[100:109],
phenotype="imaginary")
gcs1
## or with color...[＃或彩色......]
gcs2 <- GeneColorSet(sample.ExpressionSet[100:109],
phenotype="imaginary",
geneColor=factor(
rep(c("up", "down", "unchanged"),
length.out=10)),
phenotypeColor=factor(
rep(c("enhanced", "reduced"),
length.out=10)))
coloring(gcs2)
## recode geneColor of genes 1 and 4[＃重新编码基因1和4 geneColor]
coloring(gcs2)[c(1,4),"geneColor"] <- "down"
coloring(gcs2)
## reset, this time by gene name[＃复位，这个时间由基因名称]
coloring(gcs2)[c("31339_at", "31342_at"),"geneColor"] <- c("up", "up")
## usual 'factor' errors and warning apply:[＃平常“因素”错误和警告适用于：]
coloring(gcs2)[c("31339_at", "31342_at"),"geneColor"] <- c("UP", "up")
gcs2[["31342_at"]]
try(gcs2[["31342_"]]) # no partial matching[没有部分匹配]
gcs2$"31342" # 1 partial match ok[1部分比赛确定]
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。
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发表于 2012-2-25 21:16:07
