# # # R代码从装饰图案来源的小插曲AGDEX /本月/ doc / AGDEX。rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:选择# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #选项(宽度= 60)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:AGDEX包和数据加载# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(AGDEX)数据(human.data) #载入人类。数据ExpressionSet对象头(exprs (human.data)[1:5]) #预览人类表达数据头(pData (human.data)) #预览人类表型数据表(pData (human.data)美元grp) #看到每组数量(rownames (pData (human.data)) = = colnames (exprs (human.data))) #检查表达数据和表型数据样本在同一订单数据(gset.data) # GeneSetCollection人类。数据#现在对鼠标一样。数据数据(mouse.data)头(exprs (mouse.data)[1:5])头(pData (mouse.data))表(pData (mouse.data)美元grp)所有(colnames (exprs (mouse.data)) = = rownames (pData (mouse.data))) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:准备敏捷。设置对象的# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #创建敏捷。设置human.comparison dex.set。< - make.dex.set.object (Eset.data =人类。数据,comp.var = 2, comp.def =“human.tumor.typeD-other.human.tumors gset.collection = dex.set gset.data)。鼠标< - make.dex.set.object (mouse.data comp.var = 2, comp.def =“mouse.tumor-mouse.control gset.collection = NULL) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:说明结构的地图。数据对象# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #数据(map.data)名称(map.data)头(map.data probe.map美元)map.data map.Aprobe美元。坳map.data map.Bprobe美元。坳# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:AGDEX分析# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # agdex.res < -agdex (dex.setA = dex.set。人类,dex.setB = dex.set。鼠标,map.data =地图。数据,min.nperms = 5, max.nperms = 10) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:AGDEX结果对象# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #名称(agdex.res) agdex.res dex.compA #回声comp.def美元的敏捷。刚毛agdex.res dex.compB #回声comp.def美元的敏捷。setB头(agdex.res dex.asgnA美元)#回声从敏捷归类标签。刺毛的头(agdex.res dex.asgnB美元)#回声从敏捷归类标签。setB ################################################### ### code chunk number 7: Differential Expression Analysis Results ################################################### head(agdex.res$dex.resA) # Human results, difference of means and p-values head(agdex.res$dex.resB) # Mouse Results, difference of means and p-values ################################################### ### code chunk number 8: Meta-Analysis Results ################################################### head(agdex.res$meta.dex.res) ################################################### ### code chunk number 9: AGDEX.rnw:203-204 ################################################### agdex.scatterplot(agdex.res, gset.id=NULL) ################################################### ### code chunk number 10: Genome-Wide Result ################################################### agdex.res$gwide.agdex.res ################################################### ### code chunk number 11: Gene-Set Results ################################################### head(agdex.res$gset.res) ################################################### ### code chunk number 12: get result of gene-sets details ################################################### gset.res.stats<-get.gset.result.details(agdex.res, gset.ids = NULL, alpha=0.01) names(gset.res.stats) head(gset.res.stats$enrichA.details) head(gset.res.stats$agdex.details) dna.cat.process.gset.res<-get.gset.result.details(agdex.res, gset.ids="DNA_CATABOLIC_PROCESS") head(dna.cat.process.gset.res$agdex.details)