simplifyGeneFunSummary(GeneAnswers)
simplifyGeneFunSummary()所属R语言包：GeneAnswers
Simplify the significant ontology terms to a miniSet annotation
简化了显着的本体术语到miniSet注释
译者：生物统计家园网 机器人LoveR
描述----------Description----------
Simplify the significant ontology terms to a mini-set, which includes the non-overlapping most significant terms and some other ontology terms, which have direct gene mapping but not included in the significant ontology terms.
简化一个小型集，其中包括非重叠的最显着的条款和一些其他的本体而言，它有直接的基因图谱，但不包括在重大本体条款的重大本体条款。
用法----------Usage----------
simplifyGeneFunSummary(geneFunSummarizeTestInfo, Onto.graph.closure, allOntoID.direct = NULL, fdr.adjust = "none", p.value.th = 10^-5)
参数----------Arguments----------
参数：geneFunSummarizeTestInfo
the output of geneFunSummarize function
geneFunSummarize函数的输出
参数：Onto.graph.closure
a graphNEL object, whose edges represent the link between a ontology term and its offspring ontology terms
1 graphNEL对象，其边缘之间的本体术语和其后代本体术语的链接
参数：allOntoID.direct
a vector of ontology IDs which has direct gene association. If not NULL, it will be used to filter the significant ontology terms
有直接关联基因本体标识向量。如果不为NULL，它将被用于过滤的重大本体条款
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：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
值----------Value----------
The function return is a list with the same length of input "geneFunSummarizeTestInfo". Each element of the list is the simplified summarization of a gene. The simplified gene summarization is also a list with the following items
函数返回的是一个相同长度的输入“geneFunSummarizeTestInfo”的名单。列表中的每个元素是一个基因的简化概括。简化的基因总结，也是一个与下列项目列表
参数：keptSigOntoID
the significant ontology terms kept in the miniSet annotation
在保持的miniSet注释条款的重大本体
参数：keptEvidences
the non significant ontology terms which has direct gene mapping but are not the offspring of the ontology terms in keptSigOntoID
非重大本体方面具有直接的基因图谱，但不是在keptSigOntoID本体的后代
参数：scores
the annotation scores of all ontology terms in the miniSet annotation
所有本体条款在miniSet注释注释分数
The gene summarization object also includes the attributes of "pValueT".
基因概括对象还包括的属性“pValueT”。
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 geneFunSummarize
plotGeneFunSummary和geneFunSummarize
举例----------Examples----------
data(DO)
## test all ontology terms related with gene 643387[＃测试所有本体643387与基因相关条款。]
geneSummary <- geneFunSummarize('643387', gene2DO.map, DO.graph.closure.gene, 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
## simplify the annotation as a miniSet annotaiton[＃简化作为miniSet annotaiton的注解]
geneSummary.sim <- simplifyGeneFunSummary(geneSummary, DO.graph.closure.gene, p.value.th=10^-5)
geneSummary.sim
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。
|
发表于 2012-2-25 18:42:19
