os.data=function(id) { test=get(paste("LUAD.sample.test",id,sep="")) sample.info=get(paste("dataset",id,".clinical",sep="")) if(id==1) { sample.info=sample.info[,test] start=gsub("surgery date: ","",sample.info[5,]) end=gsub("vital date: ","",sample.info[8,]) os=as.numeric(as.Date(end)-as.Date(start))/30 # day status=as.numeric(gsub("dead: ","",sample.info[9,])) }else if( id==2) { sample.info=sample.info[test,] os=as.numeric(sample.info[,"Characteristics.overall.survival"]) status=ifelse(sample.info[,"Characteristics.organism.status"]=="dead at endpoint",1,0) }else if(id==3) { sample.info=sample.info[test,] os=as.numeric(gsub("months_to_last_contact_or_death: ","",sample.info[,"characteristics_ch1.11"])) status=ifelse(sample.info[,"characteristics_ch1.4"]=="vital_status: Dead",1,0) }else if(id==4) { sample.info=sample.info[test,] os=as.numeric(sample.info[,"OS.time"])/30 # day status=as.numeric(sample.info[,"OS"]) }else if(id==5) { sample.info=sample.info[test,] os=as.numeric(gsub("days to determined death status: ","",sample.info[,"characteristics_ch1.1"])) status=ifelse(sample.info[,"characteristics_ch1"]=="dead: yes",1,0) }else if(id==6) { sample.info=sample.info[test,] os=as.numeric(sample.info[,"OS_Time"]) status=as.numeric(sample.info[,"OS_Status"]) } list(os,status) } survival.p1=apply(dataset1.gene.expr.fpkm[total.overlap.genes,LUAD.sample.test1],1,function(x){ os=Surv(os.data(1)[[1]],os.data(1)[[2]]) x=as.character(ifelse(x>median(x),1,-1)) if(length(unique(x))==1) { p=1 }else { p=1-pchisq(survdiff(os~x)$chisq,1) } p }) survival.p2=apply(dataset2.gene.expr[total.overlap.genes,LUAD.sample.test2],1,function(x){ os=Surv(os.data(2)[[1]],os.data(2)[[2]]) x=as.character(ifelse(x>median(x),1,-1)) if(length(unique(x))==1) { p=1 }else { p=1-pchisq(survdiff(os~x)$chisq,1) } p }) survival.p3=apply(dataset3.gene.expr[total.overlap.genes,LUAD.sample.test3],1,function(x){ os=Surv(os.data(3)[[1]],os.data(3)[[2]]) x=as.character(ifelse(x>median(x),1,-1)) if(length(unique(x))==1) { p=1 }else { p=1-pchisq(survdiff(os~x)$chisq,1) } p }) survival.p4=apply(dataset4.gene.expr[total.overlap.genes,LUAD.sample.test4],1,function(x){ os=Surv(os.data(4)[[1]],os.data(4)[[2]]) x=as.character(ifelse(x>median(x),1,-1)) if(length(unique(x))==1) { p=1 }else { p=1-pchisq(survdiff(os~x)$chisq,1) } p }) mmpc2 <-MMPC(Surv(os.data(2)[[1]],os.data(2)[[2]]), convert(dataset2.gene.expr[variables1,LUAD.sample.test2]),test = "censIndCR",threshold = 0.2) res2=mmpc.model(Surv(os.data(2)[[1]],os.data(2)[[2]]),convert(dataset2.gene.expr[variables1,LUAD.sample.test2]) , mmpcObject = mmpc2) pred.2=predict(res3[[1]],as.data.frame(convert(dataset3.gene.expr[variables1,LUAD.sample.test3])))