# # # R代码从装饰图案的DrugVsDisease来源。Rnw的utf - 8编码:# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:DrugVsDisease。Rnw: 29 - 30日# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #选项(宽度= 60)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:DrugVsDisease。Rnw: 37-39 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(DrugVsDisease) profileAE < -generateprofiles(加入输入=“AE”=“e -大地测量学- 22528”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:DrugVsDisease。Rnw: 44-45 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #名称(profileAE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:DrugVsDisease。Rnw: 50-51 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # colnames (profileAE ranklist美元)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:DrugVsDisease。Rnw: 56-57 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # selprofiles < -selectrankedlists (profileAE, 1) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:DrugVsDisease。Rnw: 63 - 64 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #默认< -classifyprofile (data = selprofiles ranklist美元,signif.fdr = 1.1) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:DrugVsDisease。Rnw: 66 - 69 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(xtable)默认< -as.data.frame(默认[[1]])xtable(默认[2:4])# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:AEx (eval = FALSE)成分股# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # profileAE < -generateprofiles(加入输入=“AE”=“e -大地测量学- 22528”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块9号:地理(eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # gds1479 < -generateprofiles(加入“地理”=“gds1479”, # #注释=“hgu133a factorvalue =“标本”,例=“疾病”)# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块10号:DrugVsDisease。Rnw: 120 - 121 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # sel1479 < -selectrankedlists (gds1479 c(3、18)) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块11号:DrugVsDisease。Rnw: 123 - 124 # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # sel22528 < -selectrankedlists (profileAE, 1) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块12号:DrugVsDisease。Rnw: 137 - 138 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #默认< -classifyprofile (data = sel22528 ranklist美元,signif.fdr = 1.1) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块13号:DrugVsDisease。Rnw: 153 - 155 (eval = FALSE) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # c1 < -classifyprofile(数据= sel22528 ranklist美元,类型=“固定”,lengthtest = 100, # # cytoout = FALSE, noperm = 100) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块14号:DrugVsDisease。Rnw:160-162 (eval = FALSE) ################################################### ## c2<-classifyprofile(data=sel22528$ranklist,type="range",range=c(100,200), ## cytoout=FALSE,noperm=100) ################################################### ### code chunk number 15: DrugVsDisease.Rnw:166-168 (eval = FALSE) ################################################### ## c3<-classifyprofile(data=sel22528$ranklist,pvalues=sel22528$pvalues, ## cytoout=FALSE,type="dynamic",dynamic.fdr=0.5,adj="BH") ################################################### ### code chunk number 16: DrugVsDisease.Rnw:177-179 (eval = FALSE) ################################################### ## dynamicfdr<-classifyprofile(data=sel22528$ranklist,pvalues=sel22528$pvalues, ## cytoout=FALSE,type="dynamic",dynamic.fdr=0.5,signif.fdr=0.15,adj="BH") ################################################### ### code chunk number 17: DrugVsDisease.Rnw:187-189 (eval = FALSE) ################################################### ## clusteraverage<-classifyprofile(data=sel22528$ranklist,cytoout=FALSE, ## clustermethod="average",avgstat="median") ################################################### ### code chunk number 18: DrugVsDisease.Rnw:196-203 ################################################### data(customDB,package="DrugVsDisease") data(customClust,package="DrugVsDisease") data(customedge,package="DrugVsDisease") data(customsif,package="DrugVsDisease") customRefData<-classifyprofile(data=sel22528$ranklist, lengthtest=100, customRefDB=customDB, customClusters=customClust, customedge=customedge, customsif=customsif, cytoout=FALSE,signif.fdr=1.1) ################################################### ### code chunk number 19: DrugVsDisease.Rnw:209-211 (eval = FALSE) ################################################### ## CytoOut<-classifyprofile(data=sel22528$ranklist,cytoout=TRUE, ## cytofile="CytoscapeOutput",adj="BH")