dist/doc/intro.R

In jiayouzytx/StatComp21056: Select gene variables by Annovar

## ----eval=FALSE---------------------------------------------------------------
#  myqc<-function(df,pp2,cadd,sift){
#    #one
#    #select nonsynonymous
#    nonsyno <- df[which(df$V2 == "nonsynonymous SNV" ),3:8] #2891 6
#    id_syno <-paste(paste(paste(paste(nonsyno$V4,nonsyno$V5,sep = ":"),nonsyno$V6,sep = "-"), nonsyno$V7,sep = "_"), nonsyno$V8, sep = "_")
#    nonsyno[,7] <- id_syno
#    colnames(nonsyno)[7] <- "V9"
#  
#    #two
#    colnames(pp2)[1] <- "chr"
#    selected_nonsyno_1 <-pp2[which(pp2$Start %in% nonsyno$V5),] # 8852    7
#    id_sn <-paste(paste(paste(paste(selected_nonsyno_1$chr,selected_nonsyno_1$Start,sep = ":"),
#                              selected_nonsyno_1$End,sep = "-"), selected_nonsyno_1$Ref,sep = "_"), selected_nonsyno_1$Alt, sep = "_")
#    selected_nonsyno_1[,8] <- id_sn
#    colnames(selected_nonsyno_1)<-c("V1","V2","V3","V4","V5","V6","V7","V8")
#    selected_nonsyno_2 <- selected_nonsyno_1[which(selected_nonsyno_1$V8 %in% nonsyno$V9),] #810   8
#  
#    #three
#    #CADD
#    colnames(cadd)[1] <- "chr"
#    selected_nonsyno_3 <-cadd[which(cadd$Start %in% nonsyno$V5),] # 9540    7
#    id_cadd <-paste(paste(paste(paste(selected_nonsyno_3$chr,selected_nonsyno_3$Start,sep = ":"),
#                                selected_nonsyno_3$End,sep = "-"), selected_nonsyno_3$Ref,sep = "_"), selected_nonsyno_3$Alt, sep = "_")
#    selected_nonsyno_3[,8] <- id_cadd
#    colnames(selected_nonsyno_3)<-c("V1","V2","V3","V4","V5","V6","V7","V8")
#    selected_nonsyno_4 <- selected_nonsyno_3[which(selected_nonsyno_3$V8 %in% nonsyno$V9),] #[1] 827   8
#  
#    #four
#    #sift
#    colnames(sift)[1] <- "chr"
#    selected_nonsyno_5 <-sift[which(sift$Start %in% nonsyno$V5),]  # 9059    7
#    id_sift <-paste(paste(paste(paste(selected_nonsyno_5$chr,selected_nonsyno_5$Start,sep = ":"),
#                                selected_nonsyno_5$End,sep = "-"), selected_nonsyno_5$Ref,sep = "_"), selected_nonsyno_5$Alt, sep = "_")
#    selected_nonsyno_5[,8] <- id_sift
#    colnames(selected_nonsyno_5)<-c("V1","V2","V3","V4","V5","V6","V7","V8")
#    selected_nonsyno_6 <- selected_nonsyno_5[which(selected_nonsyno_5$V8 %in% nonsyno$V9),] # 790   8
#  
#    S2<-selected_nonsyno_2[,6:8] #810 3
#    S4<-selected_nonsyno_4[,6:8] #827 3
#    S6<-selected_nonsyno_6[,6:8] #790 3
#  
#    zhname0<-rbind(as.matrix(S2[,3]),as.matrix(S4[,3]),as.matrix(S6[,3])) #810+827+790=2427
#    zhname<-unique(zhname0)
#    kkk<-length(zhname)#827
#  
#    Table<-matrix(0,kkk,5)
#    Table[,1]<-zhname
#    #Table[,2]=pp2
#    for(i in 1:kkk){
#      n<-Table[i,1]
#      k<-which(S2[,3]==n)
#      if(length(k)!=0){
#        Table[i,2]=S2[k,2]
#      }else{
#        Table[i,2]=0
#      }
#    }
#    #Table[,3]=cadd
#    for(i in 1:kkk){
#      n<-Table[i,1]
#      k<-which(S4[,3]==n)
#      if(length(k)!=0){
#        Table[i,3]=S4[k,2]
#      }else{
#        Table[i,3]=0
#      }
#    }
#    #Table[,4]=sift
#    for(i in 1:kkk){
#      n<-Table[i,1]
#      k<-which(S6[,3]==n)
#      if(length(k)!=0){
#        Table[i,4]=S6[k,2]
#      }else{
#        Table[i,4]=0
#      }
#    }
#    #score to 0,1
#    for(i in 1:kkk){
#      if(Table[i,2]=="D"){
#        Table[i,2]=1
#      }else{
#        Table[i,2]=0
#      }
#    }
#    for(i in 1:kkk){
#      if(as.numeric(Table[i,3])>40){
#        Table[i,3]=1
#      }else{
#        Table[i,3]=0
#      }
#    }
#    for(i in 1:kkk){
#      if(Table[i,4]=="D"){
#        Table[i,4]=1
#      }else{
#        Table[i,4]=0
#      }
#    }
#    #
#    for(i in 1:kkk){
#      Table[i,5]=as.numeric(Table[i,2])+as.numeric(Table[i,3])+as.numeric(Table[i,4])
#    }
#    kk<-which(as.numeric(Table[,5])>=2)
#    nonsyno_Final<-Table[kk,1] #223
#    #six
#    nonsyno2<-df2[which(df$V2 == "nonsynonymous SNV" ),c(3:8,11)]  #V11:rs   2891 7
#    id_syno2 <-paste(paste(paste(paste(nonsyno2$V4,nonsyno2$V5,sep = ":"),nonsyno2$V6,sep = "-"), nonsyno2$V7,sep = "_"), nonsyno2$V8, sep = "_")
#    nonsyno2[,8] <- id_syno2
#    colnames(nonsyno2)[8] <- "V9"
#    kk<-matrix(0,length(nonsyno_Final),1)
#    for(i in 1:length(nonsyno_Final)){
#      t<-nonsyno_Final[i]
#      k<-which(nonsyno2$V9==t)
#      kk[i]<-k
#    }
#    Allrs<-nonsyno2[kk,7]
#    return(Allrs)
#  }
#  

## ----eval=FALSE---------------------------------------------------------------
#  function(pheno,dygx){
#    dygx1<-dygx[,1:2]
#    nn<-dim(pheno)[1]
#    for(i in 1:nn)
#    {
#      k1<-pheno$names[i]
#      k2<-which(dygx1[,2]==k1)
#      pheno$names[i]<-dygx1[k2,1]
#    }
#    id.pheno <- pheno[,"names"]
#    v0<-as.factor(id.pheno)
#    K<-length (levels (v0) )
#    v1<- vector(mode="character", K)
#    v1[1]<-id.pheno[1]
#    k=1
#    for (i in 2:length(v0))
#    {
#      if(id.pheno[i]!=id.pheno[i-1])
#      {
#        k=k+1
#        v1[k]=id.pheno[i]
#      }
#    }
#    v2<-table(v0)
#    v3<-v2[v1]
#    return(v3)
#  }