getHOMOLOG(annotationTools)
getHOMOLOG()所属R语言包：annotationTools
Find homologous/orthologous gene (ID)
找到同源/同源基因（ID）
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Takes a vector of gene IDs, a table of homologs/orthologs, and a target species and returns gene IDs corresponding to homologous/orthologous genes.
注意到，表/同源同源基因标识向量和目标物种和回报基因标识对应的同源基因同源/。
用法----------Usage----------
getHOMOLOG(geneid, targetspecies, homol, cluster = FALSE, diagnose = FALSE, noIDsymbol = NA, clusterCol = 1, speciesCol = 2, idCol = 3)
参数----------Arguments----------
参数：geneid
character vector containing gene IDs.
字符向量基因标识。
参数：targetspecies
identifier of the target species in the homology/orthology table.
目标物种的同源性/直向表标识符。
参数：homol
homology/orthology table (data frame) listing gene IDs (1 per line) along with the species and the homology/orthology cluster they belong to.
同源/直向表（数据框）上市的基因标识（每行1）随着物种的同源性/直向聚类，它们都属于。
参数：cluster
logical. If TRUE, the identifiers provided in 'geneid' are homology/orthology cluster IDs. If FALSE, they are gene IDs.
逻辑。如果是TRUE，geneid“提供的标识符是同源/的直向聚类ID。如果为FALSE，它们是基因标识。
参数：diagnose
logical. If TRUE, 3 (logical) vectors used for diagnostic purpose are returned in addition to the annotation. If FALSE (default) only the annotation is returned.
逻辑。如果是TRUE，返回3（逻辑）用于诊断目的的向量在另外的注解。如果为FALSE（默认）的注释，则返回。
参数：noIDsymbol
character string to be used in output list 'targetid' if no homologous/orthologous gene is found or provided in the annotation table.
在输出列表“目标ID”用于字符串，如果没有同源/同源基因的发现或注释表中提供的。
参数：clusterCol
column in homology/orthology table containing homology/orthology cluster IDs.
列同源性/直向同源/的直向聚类ID表。
参数：speciesCol
column in homology/orthology table containing species IDs.
列同源性/直向表包含物种的ID。
参数：idCol
column in homology/orthology table containing gene IDs.
同源/直向含有基因标识的表列中。
Details
详情----------Details----------
The homology/orthology table lists gene IDs (from several species) and the homology/orthology cluster they belong to. Homologous and orthologous genes share a common cluster identifier. Given a certain gene ID, a target species, and a homology/orthology table, all gene IDs belonging to the same homology/orthology cluster and to the specified target species are returned. If 'targetspecies' is the species 'geneid' belongs to, by definition, homologous genes are returned (if listed). On the contrary, specifying a 'targetspecies' different from the host species 'geneid' belongs to, results in orthologous genes to be returned. Note that each gene ID is assumed to be unique and to belong to a single homology/orthology cluster.
同源/直向表列出了基因识别码（从几个物种）和他们所属的同源性/直向聚类。同源性和同源基因都有一个共同的簇标识符。由于某种基因ID，目标物种，和同源性/直向表，所有属于相同的同源性/直向聚类，并返回指定的目标物种的基因标识。如果targetspecies是物种“geneid”属于定义，返回同源基因（如已上市）。相反，指定一个targetspecies“主机物种geneid”不同，属于同源基因的结果要返回。请注意，每一个基因的ID被认为是独特的，属于一个单一的同源性/直向聚类。
Gene IDs of homologous/orthologous genes are returned as elements of list 'targetid'. If multiple (homologous/orthologous) gene IDs are provided for 'geneid[i]', a vector containing all gene IDs is returned as the 'i-th' element of list 'targetid'.
基因同源基因同源/返回的ID为“目标ID”列表中的元素。如果多个基因（同源/直系）的ID为“geneid [i]的规定，则返回一个向量包含所有基因的ID”第i个“目标ID”列表中的元素。
Default values for 'clusterCol', 'speciesCol', and 'idCol' are chosen to match the table provided by HomoloGene (homologene.data provided by www.ncbi.nlm.nih.gov/HomoloGene). Homology/orthology tables from other sources might require setting these values appropriately.
“clusterCol，speciesCol，idCol”的默认值是选择匹配HomoloGene（homologene.data www.ncbi.nlm.nih.gov / HomoloGene）提供的表。从其他来源的同源性/直向表的可能需要适当设置这些值。
If 'cluster' is TRUE, cluster IDs can be provided in 'geneid' (instead of gene IDs) and the function will return all (homologous/orthologous) gene IDs belonging to a given cluster ID and a given 'targetspecies'. This can be used to mine orthology tables provided by Affymetrix (e.g. 'Mouse430\_2\_ortholog.csv') for orthologous probe set IDs (see 'examples' below).
“聚类”如果是TRUE，聚类标识可以提供geneid（而不是基因标识），该函数将返回（同源/直系）基因属于一个给定的聚类ID标识一个给定的“targetspecies”。这可以用来挖掘由Affymetrix同源探针集ID（例如Mouse430 \ _2的\ _ortholog.csv“）（见”的例子，下面）提供直向表。
值----------Value----------
参数：targetid
list of length 'length(geneid)' the 'i'-th element of which contains the homologous/orthologous gene IDs for 'geneid[i]' and 'targetspecies'.
长度长度（geneid，）列表δ-th元素，其中包含了同源/同源基因身份证“geneid [I]和targetspecies”。
参数：empty
logical vector of length 'length(geneid)'. 'empty[i]' is TRUE if 'geneid[i]' is empty or NA.
逻辑矢量长度的长度（geneid）。 “空[I]”，如果“geneid [I]为空或不适用。
参数：noentry
locial vector of length 'length(geneid)'. 'noentry[i]' is TRUE if 'geneid[i]' cannot be found in column 'idCol' (default is column 3) of the homology/orthology table 'homol'.
locial向量长度的长度（geneid）。 “NOENTRY [I]”为TRUE，如果“geneid我不能列idCol的（默认是3列）的同源性/直向表homol”的发现。
参数：notargetid
locial vector of length 'length(geneid)'. 'notargetid[i]' is TRUE if 'geneed[i]' is found in the homology/orthology table but no homolog/ortholog is listed for 'targetspecies'.
locial向量长度的长度（geneid）。 notargetid [I]是TRUE，如果geneed我发现同源性/直向表，但没有同源物/同源targetspecies“的上市。
作者（S）----------Author(s)----------
Alexandre Kuhn
举例----------Examples----------
##example Homologene file and its location[＃例如Homologene文件和它的位置]
homologeneFile<-system.file('extdata','homologene_part.data',package='annotationTools')
##load Homologene file[＃加载Homologene文件]
homologene<-read.delim(homologeneFile,header=FALSE)
##get mouse (species ID 10090) orthologs of several human (species ID 9606) gene ID (among those: 5982, gene symbol RFC2 and 93587, gene symbol: RG9MTD2)[＃鼠标的几个人的（品种编号10090）同源基因（品种编号9606）的ID（在那些：5982，RFC2和93587基因符号，基因符号：RG9MTD2）]
myGenes<-c(5982,93587,NA,100)
getHOMOLOG(myGenes,10090,homologene)
##track origin of annotation failure for the last 2 gene IDs[＃最后2基因的ID追踪注解失败的起源]
getHOMOLOG(myGenes,10090,homologene,diagnose=TRUE)
##get mouse gene belonging to homologene cluster IDs 6885 and 6886[＃小鼠基因属于homologene聚类的ID 6885和6886]
myClusters<-c(6885,6886)
getHOMOLOG(myClusters,10090,homologene,cluster=TRUE)
##mine Affymetrix (example) ortholog file[＃矿Affymetrix公司（例如）同源文件]
affyOrthologFile<-system.file('extdata','HG-U133_Plus_2_ortholog_part.csv',package='annotationTools')
affyOrthologs<-read.csv(affyOrthologFile,colClasses='character')
##get Mouse430_2 probe set IDs 'orthologous' to HG-U133_Plus_2 probe set IDs 1053_at and 121_at[＃得到Mouse430_2探针组ID来HG-U133_Plus_2探针同源设置标识1053_at和121_at的]
myPS<-c('1053_at','121_at')
getHOMOLOG(myPS,'Mouse430_2',affyOrthologs,cluster=TRUE,clusterCol=1,speciesCol=4,idCol=3)
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。
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发表于 2012-2-25 11:59:42
