GeneAnswers-class(GeneAnswers)
GeneAnswers-class()所属R语言包：GeneAnswers
Class GeneAnswers: contain and describe the relationship between given gene data and specified category
类GeneAnswers：包含和描述给定的基因数据，并指定类别之间的关系
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This is a class representation of the relationship between given gene data and specified category.
这是一个给定的基因数据，并指定类别之间的关系类表示。
创建对象----------Creating Objects----------
Objects can be created using the function geneAnswersBuilder.
创建对象可以使用的功能geneAnswersBuilder。
插槽----------Slots----------
Slot specific to GeneAnswers:
GeneAnswers插槽具体：
geneInput: a data frame containing gene Entrez IDs with or without any values. Current version only supports gene Entrez IDs. The values could be foldChange, p value, or other values. These data can be used for concept-gene network. Genes with positive values will be represented as red nodes, while negative value genes are green nodes.
geneInput：一个数据框的基因Entrez的标识或不包含任何值。当前版本只支持基因Entrez的标识。值可以是foldChange，p值，或其他值。这些数据可以用于概念的基因网络。正面的价值观的基因将被表示为红色的节点，而负值基因都是绿色的节点。
testType: statistical test method. Current version supports hypergeometric test to test relationship between genes and specified categories.
testType：统计检验方法。当前版本支持超几何测试，测试基因与特定类别之间的关系。
pvalueT: the cutoff value of statistical test. Any categories will not be reported if the p value is more than the cutoff.
pvalueT：统计检验的临界值。任何类别将不会被报道，如果p值超过截止。
genesInCategory: a list containing genes belonging to categories. The names of the list are categories.
genesInCategory：一个列表，其中包含的基因属于类别。名单上的名字类别。
geneExprProfile: a data frame to store gene expression data. If not available, it could be NULL.
geneExprProfile：基因表达数据存储数据框。如果没有可用的，它可以是NULL。
annLib: annotation database used for statistical test.
annLib：注释的数据库，用于统计检验。
categoryType: functional or medical category used for statistical test.
categoryType：统计测试使用的功能或医疗类。
enrichmentInfo: a data frame containing filtered categories with statistical results by specified pvalueT.
enrichmentInfo：一个数据框包含过滤类别与指定pvalueT统计结果。
方法----------Methods----------
Class-specific methods:
类的具体方法：
getGeneInput(GeneAnswers): Access the geneInput slot of GeneAnswers object.
getGeneInput(GeneAnswers)：进入GeneAnswers对象的geneInput插槽。
getTestType(GeneAnswers): Access the testType slot of GeneAnswers object.
getTestType(GeneAnswers)：进入GeneAnswers对象testType的插槽。
getPValueT(GeneAnswers): Access the pvaluteT slot of GeneAnswers object.
getPValueT(GeneAnswers)：进入GeneAnswers对象pvaluteT的插槽。
getGenesInCategory(GeneAnswers): Access the genesInCategory slot of GeneAnswers object.
getGenesInCategory(GeneAnswers)：进入GeneAnswers对象genesInCategory的插槽。
getGeneExprProfile(GeneAnswers): Access the geneExprProfile slot of GeneAnswers object.
getGeneExprProfile(GeneAnswers)：进入GeneAnswers对象的geneExprProfile插槽。
getAnnLib(GeneAnswers): Access the annLib slot of GeneAnswers object.
getAnnLib(GeneAnswers)：进入GeneAnswers对象annLib的插槽。
getCategoryType(GeneAnswers): Access the categoryType slot of GeneAnswers object.
getCategoryType(GeneAnswers)：进入GeneAnswers对象categoryType的插槽。
getEnrichmentInfo(GeneAnswers): Access the enrichmentInfo slot of GeneAnswers object.
getEnrichmentInfo(GeneAnswers)：进入GeneAnswers对象enrichmentInfo的插槽。
setGeneInput(GeneAnswers, geneInput): Assign the geneInput slot of GeneAnswers object.
setGeneInput(GeneAnswers, geneInput)：分配的GeneAnswers对象geneInput插槽。
setTestType(GeneAnswers, type=c('hyperG', 'none')): Assign the testType slot of GeneAnswers object.
setTestType(GeneAnswers, type=c('hyperG', 'none'))：分配的GeneAnswers对象testType插槽。
setPValueT(GeneAnswers, pvalueT): Assign the pvaluteT slot of GeneAnswers object.
setPValueT(GeneAnswers, pvalueT)：分配的GeneAnswers对象pvaluteT插槽。
setGenesInCategory(GeneAnswers, genesInCategory): Assign the genesInCategory slot of GeneAnswers object.
setGenesInCategory(GeneAnswers, genesInCategory)：分配的GeneAnswers对象genesInCategory插槽。
setGeneExprProfile(GeneAnswers, geneExprProfile): Assign the geneExprProfile slot of GeneAnswers object.
setGeneExprProfile(GeneAnswers, geneExprProfile)：GeneAnswers对象geneExprProfile插槽分配。
setAnnLib(GeneAnswers, annLib): Assign the annLib slot of GeneAnswers object.
setAnnLib(GeneAnswers, annLib)：分配的GeneAnswers对象annLib插槽。
setCategoryType(GeneAnswers, type=c('GO', 'GO.BP', 'GO.CC', 'GO.MF', 'DOLITE', 'KEGG', 'REACTOME.PATH', 'CABIO.PATH', 'User defiend')): Assign the categoryType slot of GeneAnswers object.
setCategoryType(GeneAnswers, type=c('GO', 'GO.BP', 'GO.CC', 'GO.MF', 'DOLITE', 'KEGG', 'REACTOME.PATH', 'CABIO.PATH', 'User defiend'))：分配的GeneAnswers对象categoryType插槽。
setEnrichmentInfo(GeneAnswers, enrichmentInfo): Assign the enrichmentInfo slot of GeneAnswers object.
setEnrichmentInfo(GeneAnswers, enrichmentInfo)：分配的GeneAnswers对象enrichmentInfo插槽。
summary(GeneAnswers): Briefly summarize the information of GeneAnswers object and show contents of GeneAnswers object.
summary(GeneAnswers)：GeneAnswers对象和节目内容的GeneAnswers对象的信息简要总结。
show(GeneAnswers): Briefly show contents of GeneAnswers object.
show(GeneAnswers)：简单显示GeneAnswers对象的内容。
作者（S）----------Author(s)----------
Gang Feng, Pan Du and Simon Lin
参考文献----------References----------
<h3>See Also</h3> <code>geneAnswersBuilder</code>
举例----------Examples----------
data('humanExpr')
data('humanGeneInput')
x <- geneAnswersBuilder(humanGeneInput, 'org.Hs.eg.db', categoryType='GO.BP', testType='hyperG', pvalueT=0.01, FDR.correct=TRUE, geneExpressionProfile=humanExpr)
class(x)
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 18:37:06
