Ns126:Calendar/NOTES/2015-6-25: Difference between revisions

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     data1<-data[-NaRAW,]
     data1<-data[-NaRAW,]
   }else{
   }else{
     data1<-data;
     data1<-data
   }
   }
   data1}   
   data1
}   
map<-read.table("/home/sguo/annotation/GPL13534.sort.bed",as.is=T,sep="\t")
map<-read.table("/home/sguo/annotation/GPL13534.sort.bed",as.is=T,sep="\t")
pdf("correlationbetweencancers.pdf")
pdf("correlationbetweencancers.pdf")

Revision as of 01:19, 26 June 2015

It is very interesting result: 1) cancer have two peak 2) cancer have more higher correction regions

</nowiki>

RawNARemove<-function(data,missratio=0.3){

 threshold<-(missratio)*dim(data)[2]
 NaRaw<-which(apply(data,1,function(x) sum(is.na(x))>threshold))
 zero<-which(apply(data,1,function(x) all(x==0))==T)
 NaRAW<-c(NaRaw,zero)
 if(length(NaRAW)>0){
   data1<-data[-NaRAW,]
 }else{
   data1<-data
 }
 data1

} map<-read.table("/home/sguo/annotation/GPL13534.sort.bed",as.is=T,sep="\t") pdf("correlationbetweencancers.pdf") mfrow=c(4,4) corcal<-function(data){ data<-RawNARemove(data) head(map) map<-map[map[,4] %in% rownames(data),] a<-map[,2] i=1 tmp<-c() rlt<-c() index<-0 while(i < length(a)){

 start=a[i]
 end=a[i+1]
 end-start
 if(end-start<100){
   tmp<-c(tmp,i)
   i=i+1
 }else{
   if(length(tmp)>4){
     index=index+1
     tmp<-c(min(tmp),max(tmp),length(tmp),a[max(tmp)]-a[min(tmp)],round(length(tmp)/(a[max(tmp)]-a[min(tmp)]),4))
     rlt<-rbind(rlt,tmp)
   }
   tmp<-c()
   i=i+1
 }

}

 newdata<-data[match(map[,4],rownames(data)),]
 library("impute")
 newdata<-impute.knn(newdata)$data
 
 cor<-c()
 for(j in 1:nrow(rlt)){
   cor1<-mean(cor(t(newdata[rlt[j,1]:rlt[j,2],seq(1,ncol(newdata),by=2)]),use="complete.obs")) # cancer
   cor2<-mean(cor(t(newdata[rlt[j,1]:rlt[j,2],seq(2,ncol(newdata),by=2)]),use="complete.obs")) # normal
   tmp<-c(cor1,cor2)
   cor<-rbind(cor,tmp)
 }
 plot(density(cor[,1]),xlim=c(0,1),ylim=c(0,3.5),lwd=3,col="red",main="")
 lines(density(cor[,2]),xlim=c(0,1),ylim=c(0,3.5),lwd=3,col="blue",main="")
 legend("topright",legend=c("cancer","normal"),col=c("red","blue"),lwd=3,lty=1,bty="n")

} file=list.files(pattern="*.pair.RData") for(i in 1:length(file)){ load(file[i]) corcal(data) print(file[i]) } dev.off()</nowiki>