geneFunSummarize(GeneAnswers)
geneFunSummarize()所属R语言包：GeneAnswers
Summarize gene functions (annotations) based collective annotation evidences associated with ontology terms
总结基因的功能（注释）根据集体的注解本体术语相关的证据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Summarize gene functions (annotations) based collective annotation evidences associated with ontology terms
总结基因的功能（注释）根据集体的注解本体术语相关的证据
用法----------Usage----------
geneFunSummarize(genes, gene2Onto, Onto2offspring, rmOntoID = c("DOID:4", "DOID:63"), p.value.th = 0.01, fdr.adjust = "fdr", minNumTh = 2, includeTestOnto = TRUE, directMapConstraint = FALSE)
参数----------Arguments----------
参数：genes
a vector of Entrez Gene IDs to do gene function summarization
Entrez基因向量的ID，以做基因功能汇总
参数：gene2Onto
a list gene 2 Ontology mapping (Ontology IDs, duplicated IDs are allowed, which is equivalent to multiple evidences with the same function)
列表基因本体映射（本体论的ID，重复的ID是允许的，这是具有相同的功能相当于多个证据）
参数：Onto2offspring
a list or graphNEL object shows the relations of a ontology id to all its offsprings
显示列表或graphNEL对象的本体ID关系到它的所有后代
参数：rmOntoID
some ontology ids (like root id or too general ontology ids) can be pre-removed in the estimation
一些本体IDS（如根ID或过于笼统本体IDS）可以预先在估计中删除
参数：p.value.th
the p-value threshold used to determine the significance of function enrichment
p值阈值，用于确定富集功能的意义
参数：fdr.adjust
the FDR estimation methods used to estimate the FDR of function enrichment
用于估计功能浓缩FDRFDR估计方法
参数：minNumTh
the minimum number of evidences required to claim as significant enriched ontology term
显著丰富本体术语声称需要证据的最低数量
参数：includeTestOnto
whether include the direct evidence of the testing ontology term itself
是否包括测试本体词本身的直接证据
参数：directMapConstraint
whether only consider the ontology ids with direct evidence mappings
是否只考虑直接证据映射的本体IDS
值----------Value----------
The function return is a list with the same length of input "genes". Each element of the list is the summarization of a gene. The gene summarization is also a list with the following items
函数返回的是一个与输入的“基因”的相同长度的列表。列表中的每个元素是一个基因的总结。基因的总结，也是一个与下列项目列表
参数：allEvidence
all evidences (ontology terms) related with the testing gene
所有的证据（本体术语）与测试基因有关
参数：sigOntoInfo
the significant ontology terms associated with the testing gene
本体论与测试基因相关的重大条款
参数：bestOntoInfo
the information of the most significant ontology term associated with the testing gene
信息的最重要的本体与测试基因相关的术语
The gene summarization object also includes the attributes of the input parameter settings.
基因概括对象还包括输入参数设置的属性。
作者（S）----------Author(s)----------
Pan Du, Simon Lin, Gilbert Feng, Warren Kibbe
参考文献----------References----------
参见----------See Also----------
See Also plotGeneFunSummary and simplifyGeneFunSummary
plotGeneFunSummary和simplifyGeneFunSummary
举例----------Examples----------
data(DO)
## test all ontology terms related with gene PEBP1 (Entrez Gene ID: 5037)[＃测试所有本体条款PEBP1与基因有关（Entrez基因ID：5037）]
geneSummary <- geneFunSummarize('5037', gene2DO.map, DO.graph.closure.gene, p.value.th=0.01, fdr.adjust='none')
## the p.values of all related ontology terms[＃p.values所有相关的本体条件]
pValue <- sapply(geneSummary[[1]]$sigOntoInfo, function(x) x$pValue)
pValue
## plot the relations of the summarized gene annotation[＃绘制汇总基因注解的关系]
plotGeneFunSummary(geneSummary, onto.graph=DO.graph.gene, onto.graph.closure=DO.graph.closure.gene, ID2Name=DO.terms, p.value.th=0.0001, miniSetPvalue=10^-5, saveImage=FALSE)
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 18:38:36
