Identify cluster specific network

From ZhangLabWiki
Revision as of 02:06, 16 May 2017 by >Shicheng (Created page with "library(Seurat) setwd("/media/Home_Raid1/zhl002/NAS1/RNA_seq/hiseq_020617/seurat_analysis") load("./ipsnt_33k_latest3.RData") cluster<-as.matrix(pbmc33k.merged@data[,which(pbm...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

library(Seurat) setwd("/media/Home_Raid1/zhl002/NAS1/RNA_seq/hiseq_020617/seurat_analysis") load("./ipsnt_33k_latest3.RData") cluster<-as.matrix(pbmc33k.merged@data[,which(pbmc33k.merged@ident==1)]) COR<-list() for(i in 1:26) {

 cluster<-as.matrix(pbmc33k.merged@data[,which(pbmc33k.merged@ident==i)])
 data<-(na.omit(cluster[match(as.character(pbmc33k.merged@var.genes),rownames(cluster)),]))
 CORi<-cor(t(data),method="spearman")
 print(i)

}

gene<-c() for(i in 1:nrow(COR1)){

 for(j in 1:nrow(COR1)){
   for(z in 1:26){
     SD=sd(c(COR1[i][j],COR2[i][j],COR3[i][j],
           COR4[i][j],COR5[i][j],COR6[i][j],
           COR7[i][j],COR8[i][j],COR9[i][j],
           COR10[i][j],COR11[i][j],COR12[i][j],
           COR13[i][j],COR14[i][j],COR15[i][j],
           COR16[i][j],COR17[i][j],COR18[i][j],
           COR19[i][j],COR20[i][j],COR21[i][j],
           COR22[i][j],COR23[i][j],COR24[i][j],
           COR25[i][j],COR26[i][j],na.rm=T),na.rm=T)
     if(SD>0.6){
       gene<-c(gene,i,j)
     }
   }
       
 }

}

      1. example
  1. gene<-c()
  2. for(i in 1:nrow(COR1)){
  3. print(i)
  4. for(j in 1:nrow(COR1)){
  5. for(z in 1:4){
  6. SD=try(sd(c(COR1[i,j],COR2[i,j],COR3[i,j],COR4[i,j]),na.rm=T))
  7. if(!is.na(SD) && SD>0.6){
  8. gene<-c(gene,i,j)
  9. }
  10. }
  11. }
  12. }