CoHyperGResult-class(PCpheno)
CoHyperGResult-class()所属R语言包：PCpheno
Class "CoHyperGResult"
类“CoHyperGResult”
译者：生物统计家园网 机器人LoveR
描述----------Description----------
This class represents the results of a test for over-representation of genes in a selected gene set based among protein complexes upon the Hypergeometric distribution.
这个类表示一个基因代表后，超几何分布的蛋白质复合物之间的基因组在选定的测试结果。
类的对象----------Objects from the Class----------
Objects is created by calls to the funtion hyperGTest.
对象由的funtion hyperGTest的调用在创建。
插槽----------Slots----------
pvalues: "numeric" vector: the ordered
pvalues："numeric"向量：有序
oddsRatios: Object of class "numeric"
oddsRatios类"numeric"：对象
expectedCounts: Object of class "numeric"
expectedCounts类"numeric"：对象
geneCounts: "integer" vector: for each category term tested, the number of genes from the gene set that
geneCounts："integer"向量：每个类别的术语测试，从基因的基因数量，
universeCounts: "integer" vector: for each category term tested, the number of genes from the gene
universeCounts："integer"向量：每个类别的术语测试，从基因的基因数目
catToGeneId: Object of class "list". The names of the list are category IDs. Each element is a vector of gene IDs annotated at the given category ID and in the
catToGeneId类"list"的对象。名单上的名字是类别ID。每个元素是一个基因的ID在给定的类别ID注明的向量，并在
延伸----------Extends----------
Class "HyperGResultBase", directly.
类"HyperGResultBase"，直接。
方法----------Methods----------
geneCounts signature(r = "CoHyperGResult"): return an "numeric" vector: for each category term tested, the number of genes from
geneCountssignature(r = "CoHyperGResult")：返回一个"numeric"向量：每个类别的术语测试，基因数目从
pvalues signature(r = "HyperGResult"): return a "numeric"
pvaluessignature(r = "HyperGResult")：返回一个"numeric"
oddsRatios signature(r = "HyperGResult"): return a "numeric"
oddsRatiossignature(r = "HyperGResult")：返回一个"numeric"
expectedCounts signature(r = "HyperGResult"): return a "numeric"
expectedCountssignature(r = "HyperGResult")：返回一个"numeric"
universeCounts signature(r = "HyperGResult"): return an "numeric" vector: for each category term tested, the number of genes from
universeCountssignature(r = "HyperGResult")：返回一个"numeric"向量：每个类别的术语测试，基因数目从
geneIdUniverse signature(r = "CoHyperGResult"): return a list named by the protein Complexes. Each element of the list is a vector of gene identifiers (from the gene universe) annotated at the
geneIdUniversesignature(r = "CoHyperGResult")：返回由蛋白质复合物的命名列表。列表中的每个元素为向量的基因标识（从宇宙基因）在注释
summary signature(r = "CoHyperGResult"): Returns a data.frame summarizing the test result. Optional arguments pvalue and categorySize allow specification of minimum p-value and cateogyrSize, respectively. Optional argument htmlLinks is a logical value indicating whether to add HTML links (useful in conjunction with xtables
总结signature(r = "CoHyperGResult")：返回一个data.frame总结测试结果。可选参数pvalue和categorySize允许最小p值和cateogyrSize，规范。可选参数htmlLinks是一个逻辑值，该值指示是否添加xtables结合HTML链接（有用
作者（S）----------Author(s)----------
S. Falcon and N. LeMeur
参见----------See Also----------
HyperGResultBase-class
HyperGResultBase-class
举例----------Examples----------
data(DudleyPhenoM)
data(ScISIC)
## Select genes sensitive to paraquat[＃选择基因敏感百草枯]
DudleyPhenoL <- apply(DudleyPhenoM,2,function(x) names(which(x==1)))
paraquat <- DudleyPhenoL[["Paraq"]]
## Apply a hypergeometric test[＃应用超几何试验。]
params <- new("CoHyperGParams",
geneIds=paraquat,
universeGeneIds=rownames(ScISIC),
annotation="org.Sc.sgd.db",
categoryName="ScISIC",
pvalueCutoff=0.01,
testDirection="over")
paraquat.complex <- hyperGTest(params)
## access the p-values[＃访问的P-值]
pvalues(paraquat.complex)[1:5]
## Display a summary of the results[＃显示结果摘要]
summary(paraquat.complex)[,1:4]
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 2012-2-26 10:55:58
