Ns126:Calendar/NOTES/2017-4-30: Difference between revisions

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(Replaced content with " Identify.cluster.specific.network.R")
 
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<nowiki>library(Seurat)
[[Identify cluster specific network|Identify.cluster.specific.network.R]]
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)),]))
  COR[[i]]<-cor(t(data),method="spearman")
  print(i)
}
gene<-c()
for(i in 1:nrow(COR[[1]])){
  for(j in 1:nrow(COR[[1]])){
    for(z in 1:26){
      SD=sd(c(COR[[1]][i][j],COR[[2]][i][j],COR[[3]][i][j],
            COR[[4]][i][j],COR[[5]][i][j],COR[[6]][i][j],
            COR[[7]][i][j],COR[[8]][i][j],COR[[9]][i][j],
            COR[[10]][i][j],COR[[11]][i][j],COR[[12]][i][j],
            COR[[13]][i][j],COR[[14]][i][j],COR[[15]][i][j],
            COR[[16]][i][j],COR[[17]][i][j],COR[[18]][i][j],
            COR[[19]][i][j],COR[[20]][i][j],COR[[21]][i][j],
            COR[[22]][i][j],COR[[23]][i][j],COR[[24]][i][j],
            COR[[25]][i][j],COR[[26]][i][j],na.rm=T),na.rm=T)
      if(SD>0.6){
        gene<-c(gene,i,j)
      }
    }
       
  }
}
### example
#gene<-c()
#for(i in 1:nrow(COR[[1]])){
#  print(i)
#  for(j in 1:nrow(COR[[1]])){
#    for(z in 1:4){
#      SD=try(sd(c(COR[[1]][i,j],COR[[2]][i,j],COR[[3]][i,j],COR[[4]][i,j]),na.rm=T))
#      if(!is.na(SD) && SD>0.6){
#        gene<-c(gene,i,j)
#      }
#    }
#   
#  }
#}
</nowiki>

Latest revision as of 02:06, 16 May 2017