annFUN(topGO)
annFUN()所属R语言包：topGO
Functions which map gene identifiers to GO terms
功能基因标识映射GO术语
译者：生物统计家园网 机器人LoveR
描述----------Description----------
These functions are used to compile a list of GO terms such that each element in the list is a character vector containing all the gene identifiers that are mapped to the respective GO term.
这些功能是用来编译一个列表，列表中的每个元素是一个特征向量，包含所有的基因标识符映射到各自的围棋术语的GO术语。
用法----------Usage----------
annFUN.db(whichOnto, feasibleGenes = NULL, affyLib)
annFUN.org(whichOnto, feasibleGenes = NULL, mapping, ID = "entrez")
annFUN(whichOnto, feasibleGenes = NULL, affyLib)
annFUN.gene2GO(whichOnto, feasibleGenes = NULL, gene2GO)
annFUN.GO2genes(whichOnto, feasibleGenes = NULL, GO2genes)
annFUN.file(whichOnto, feasibleGenes = NULL, file, ...)
readMappings(file, sep = "\t", IDsep = ",")
inverseList(l)
参数----------Arguments----------
参数：whichOnto
character string specifying one of the three GO ontologies, namely: "BP", "MF", "CC"
指定一个字符串的三个基因本体，即："BP"，"MF"，"CC"
参数：feasibleGenes
character vector containing a subset of gene identifiers. Only these genes will be used to annotate GO terms. Default value is NULL which means that there are no genes filtered.
字符向量基因标识的一个子集。只有这些基因将被用来注释GO术语。默认值是NULL这意味着有没有基因筛选。
参数：affyLib
character string containing the name of the Bioconductor annotaion package for a specific microarray chip.
字符串包含一个特定的基因芯片的Bioconductor annotaion包的名称。
参数：gene2GO
named list of character vectors. The list names are genes identifiers. For each gene the character vector contains the GO identifiers it maps to. Only the most specific annotations are required.
命名特征向量的名单。列表名称是基因标识。对于每一个基因的特征向量包含它映射到好标识符。只有最具体的注释。
参数：GO2genes
named list of character vectors. The list names are GO identifiers. For each GO the character vector contains the genes identifiers which are mapped to it. Only the most specific annotations are required.
命名特征向量的名单。列表名称是好标识符。对于每个GO的特征向量包含标识符映射到它的基因。只有最具体的注释。
参数：mapping
character string specifieng the name of the Bioconductor package containing the gene mappings for a specific organism. For example: mapping = "org.Hs.eg.db".
字符串specifieng Bioconductor包含有基因的名称映射为一个特定的有机体。例如：mapping = "org.Hs.eg.db"。
参数：ID
character string specifing the gene identifier to use. Currently only the following identifiers can be used: c("entrez", "genbank", "alias", "ensembl", "symbol", "genename", "unigene")
字符串specifing基因标识的使用。目前，只有下列标识符可用于：c("entrez", "genbank", "alias", "ensembl", "symbol", "genename", "unigene")
参数：file
character string specifing the file containing the annotations.
字符串specifing文件，其中包含的注解。
参数：...
other parameters
其他参数
参数：sep
the character used to separate the columns in the CSV file
字符用于分隔的CSV文件中列
参数：IDsep
the character used to separate the annotated entities
用来分隔注解实体字符
参数：l
a list containing mappings
包含映射列表
Details
详情----------Details----------
All these function restrict the GO terms to the ones belonging to the specified ontology and to the genes listed in the feasibleGenes attribute (if not empty).
所有这些功能限制到指定的本体和feasibleGenes属性（如果不为空）中列出的基因的GO术语。
The function annFUN.db uses the mappings provided in the Bioconductor annotation data packages. For example, if the Affymetrix hgu133a chip it is used, then the user should set affyLib = "hgu133a.db".
的功能annFUN.db使用Bioconductor注解数据包提供的映射。例如，如果在Affymetrix公司hgu133a芯片，它使用，那么用户应该设置affyLib = "hgu133a.db"。
The functions annFUN.gene2GO and annFUN.GO2genes are used when the user provide his own annotations either as a gene-to-GOs mapping, either as a GO-to-genes mapping.
职能annFUN.gene2GO和annFUN.GO2genes时使用的用户提供基因GOS映射，无论是作为一个GO基因定位自己的注释。
The annFUN.org function is using the mappings from the "org.XX.XX" annotation packages. The function supports different gene identifiers.
annFUN.org函数正在使用的的“org.XX.XX”注释包的映射。该功能支持不同的基因标识。
The annFUN.file function will read the annotationsof the type gene2GO or GO2genes from a text file.
annFUN.file函数将读取annotationsof的的类型gene2GO或从一个文本文件GO2genes。
值----------Value----------
A named(GO identifiers) list of character vectors.
命名名单（GO标识符）字符向量。
作者（S）----------Author(s)----------
Adrian Alexa
参见----------See Also----------
topGOdata-class
topGOdata-class
举例----------Examples----------
library(hgu133a.db)
set.seed(111)
## generate a gene list and the GO annotations[＃生成的基因名单的GO注释。]
selGenes <- sample(ls(hgu133aGO), 50)
gene2GO <- lapply(mget(selGenes, envir = hgu133aGO), names)
gene2GO[sapply(gene2GO, is.null)] <- NA
## the annotation for the first three genes[＃注释前三基因的]
gene2GO[1:3]
## inverting the annotations[＃反相注释]
G2g <- inverseList(gene2GO)
## inverting the annotations and selecting an ontology[＃反相注释，并选择一个本体]
go2genes <- annFUN.gene2GO(whichOnto = "CC", gene2GO = gene2GO)
## generate a GO list with the genes annotations[＃生成一个与基因注解的好列表]
selGO <- sample(ls(hgu133aGO2PROBE), 30)
GO2gene <- lapply(mget(selGO, envir = hgu133aGO2PROBE), as.character)
GO2gene[1:3]
## select only the GO terms for a specific ontology[＃只选择一个特定的本体GO术语]
go2gene <- annFUN.GO2genes(whichOnto = "CC", GO2gene = GO2gene)
##################################################[＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃]
## Using the org.XX.xx.db annotations[＃使用org.XX.xx.db注释，]
##################################################[＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃＃]
## GO to Symbol mappings (only the BP ontology is used)[＃符号映射（只有使用BP本体）]
xx <- annFUN.org("BP", mapping = "org.Hs.eg.db", ID = "symbol")
head(xx)
## Not run: [＃无法运行：]
allGenes <- unique(unlist(xx))
myInterestedGenes <- sample(allGenes, 500)
geneList <- factor(as.integer(allGenes
names(geneList) <- allGenes
GOdata <- new("topGOdata",
ontology = "BP",
allGenes = geneList,
nodeSize = 5,
annot = annFUN.org,
mapping = "org.Hs.eg.db",
ID = "symbol")
## 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。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。
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发表于 2012-2-26 15:42:16
