GOTermsList(goProfiles)
GOTermsList()所属R语言包:goProfiles
Functions to create and manage lists of GO terms associated with a vector of 'Entrez' identifiers
函数来创建和管理一个向量“Entrez的”标识符相关的GO术语列表
译者:生物统计家园网 机器人LoveR
描述----------Description----------
These functions prepare data to be processed by the 'basicProfile' function. To create a profile a set of GOterms belonging to one or more ontologies is needed The terms belonging to each gene must be given separately so that they can be counted. This function queries the environment 'GOENTREZID2GO' with the vector of Entrez terms and formats the output into a list whose components -one per Entrez term- contain the most specific GO identifiers associated with this term.
这些功能准备要处理的数据由“basicProfile”功能。要创建一个配置文件,需要一套属于一个或多个本体GOterms属于每个基因的条款必须分开,使他们可以算作。此功能查询到每Entrez的组件 - 一个任期内包含的最具体的好与这个词相关的标识符列表Entrez的条款和格式输出向量与环境的“GOENTREZID2GO。
用法----------Usage----------
GOTermsList(LLids, onto = "any", evid = "any", na.rm = TRUE, orgPkg )
getAncestorsLst(GOtermslist, onto, unique.ancestor=TRUE, na.rm=TRUE, combine=TRUE)
getGOLevel(onto, level)
参数----------Arguments----------
参数:LLids
Character vector of Entrez (formerly Locuslink identifiers)
特征向量Entrez(原名Locuslink标识符)
参数:onto
ontology to be queried using the genes list
本体要查询使用基因列表
参数:evid
type of evidence supporting the selected GO Terms
支持选定的GO术语的证据类型
参数:na.rm
flag indicating if those ids returning NA must be removed from the output
指示标志,必须从输出中删除,如果这些ID回覆NA
参数:orgPkg
Organism annotation package ('org.Xx.eg.db') required to obtain the GO terms associated with the Entrez identifiers
生物体注解包(“org.Xx.eg.db)需要获得Entrez的标识符相关的GO术语
参数:GOtermslist
List produced by a call to function GOTermsList
通过调用产生函数GOTermsList一览表
参数:unique.ancestor
Flag to remove repeated ancestor identifiers
标志除去重复的祖先标识符
参数:combine
Flag to combine ancestors
要结合祖先的标志
参数:level
GO level at which the profile is built
开始配置文件是建立在哪一级
Details
详情----------Details----------
During the call to this function there may appear two types of NAs.
在调用这个函数有可能出现两种类型的NAS。
By one side if a name is not mapped in LocusLink this yields an NA that must be eliminated because nothing can be found through LL about this name
一方如果名称不映射在LocusLink这会产生一个必须被淘汰的NA,因为没有什么可以通过这个名字的LL发现约
By another side if a gene is identified in LL but yields NA it seems to mean that it is not mapped in the GO
另一侧,如果一个基因确定的LL,但产量不适用这似乎意味着它不映射在GO
This may be eliminated but it may be worth the pity to keep track of them and to put these terms in an 'Seemingly unnanotated' category. In the case that its number was very high it migt suggest reviewing the list or reconsidering the results.
这可能会被淘汰,但它可能是值得怜悯,以跟踪它们在一个看似unnanotated的类别,并把这些条款。的情况下,其数量是非常高的,它migt建议检讨名单或重新考虑的结果。
值----------Value----------
A list whose components -one per Entrez term- are character vectors with the most specific GO identifiers associated with this term
列表的组件每Entrez的一个术语是与这个词相关的最具体的好标识符的字符向量
作者(S)----------Author(s)----------
Alex Sanchez
参见----------See Also----------
getAncestorsLst
getAncestorsLst
举例----------Examples----------
#data(CD4Ids)[数据(CD4Ids)]
#simpleLLids<- as.character(c(2189,5575,5569,11)) #1 is not a Locuslink identifier[simpleLLids < - as.character(C(2189,5575,5569,11))#1不是Locuslink的标识符]
#simpleGOlist<- GOTermsList (simpleLLids, orgPkg="org.Hs.eg.db")[simpleGOlist < - GOTermsList(simpleLLids,orgPkg =“org.Hs.eg.db”)]
#print(simpleGOlist.CC<-GOTermsList (simpleLLids,"CC", orgPkg="org.Hs.eg.db"))[打印(simpleGOlist.CC <GOTermsList(simpleLLids,“抄送”,“orgPkg =”org.Hs.eg.db))]
#print(simpleGOlist.IEA<-GOTermsList (simpleLLids,evid="IEA",na.rm=TRUE, orgPkg="org.Hs.eg.db"))[打印(simpleGOlist.IEA <GOTermsList,(simpleLLids,EVID =“国际能源署”,na.rm = TRUE,orgPkg =“org.Hs.eg.db”))]
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注:
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