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#calculate vdj occurence function
.calc_vdj_occ<-function(repertoire_in,name){
#make table of v,d,j_calls and calculate frequencies
occurrence_v <- as.data.frame(table(repertoire_in$v_call))
occurrence_v$Freq <- occurrence_v$Freq/sum(occurrence_v$Freq)
occurrence_v$gene <- "V"
occurrence_d <- as.data.frame(table(repertoire_in$d_call))
occurrence_d$Freq <- occurrence_d$Freq/sum(occurrence_d$Freq)
occurrence_d$gene <- "D"
occurrence_j <- as.data.frame(table(repertoire_in$j_call))
occurrence_j$Freq <- occurrence_j$Freq/sum(occurrence_j$Freq)
occurrence_j$gene <- "J"
vdj_occurrence <- rbind(occurrence_v,occurrence_d,occurrence_j)
vdj_occurrence$repertoire <- name
vdj_occurrence_df <- vdj_occurrence
vdj_occurrence_df$gene <- factor(vdj_occurrence_df$gene,levels=c("V","D","J"))
return(vdj_occurrence_df)
}
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