Project: s41467-023-44524-0 | Function: calClonalFreq (r)

system: You are an expert R programmer implementing algorithms from scientific papers.
Complete the masked function based on the algorithm description.
Follow R best practices and maintain consistent code style.
Return **only** the complete R function code.

user: Complete this R function:

**DESCRIPTION:** Calculates clonal frequency and proportion for T cell receptor sequences. Aggregates cells by TCR gene sequences to identify clonal expansions and compute their frequencies in the repertoire.

**KEY TERMS:** {
  "TCRgene": "T cell receptor gene sequence",
  "Frequency": "clone frequency",
  "Proportion": "clone proportion",
  "cloneType": "TCR clonotype definition"
}

**CONTEXT CODE:**     unique.barcode <- unique(tcr.res$barcode)
    
    complete.barcode <- c()
    for (i in seq_along(unique.barcode)){
        barcode.i <- unique.barcode[i]
        tcr.res.i <- tcr.res[which(tcr.res$barcode==barcode.i),]
        tra.i <- tcr.res.i$TCR1[!is.na(tcr.res.i$TCR1)]
        trb.i <- tcr.res.i$TCR2[!is.na(tcr.res.i$TCR2)]
        if (length(tra.i)!=0 &  length(trb.i)!=0){
            tcr.res.i.sub <- tcr.res.i[(!(is.na(tcr.res.i$TCR1)) & !(is.na(tcr.res.i$TCR2))),]
            if (nrow(tcr.res.i.sub) == 0){
                complete.barcode <- c(complete.barcode, barcode.i)
            }
        }
    }
    
    tcr.res.com <- tcr.res[which(tcr.res$barcode %in% complete.barcode),]
    return(tcr.res.com)
}


organizeTCR <- function(Con.df, tcr.res){
    for (i in seq_along(Con.df$barcode)){
        barcode.i <- Con.df$barcode[i]
        tcr.res.i <- tcr.res[which(tcr.res$barcode==barcode.i),]
        
        tcr.res.i.tra <- tcr.res.i[!(is.na(tcr.res.i$TCR1)),]
        # order rows by gene names
        if (nrow(tcr.res.i.tra) >= 3){
            tcr.res.i.tra <- tcr.res.i.tra[order(tcr.res.i.tra$umis, decreasing = TRUE),]
            tcr.res.i.tra <- tcr.res.i.tra[c(1,2),]
        }
        tcr.res.i.tra <- tcr.res.i.tra[order(nchar(tcr.res.i.tra$TCR1), tcr.res.i.tra$TCR1),]
        Con.df[which(Con.df$barcode==barcode.i),"TCR1"] <- paste(tcr.res.i.tra$TCR1,collapse = ";")
        Con.df[which(Con.df$barcode==barcode.i),"cdr3_aa1"] <- paste(tcr.res.i.tra$cdr3,collapse = ";")
        Con.df[which(Con.df$barcode==barcode.i),"cdr3_nt1"] <- paste(tcr.res.i.tra$cdr3_nt,collapse = ";")
        
        tcr.res.i.trb <- tcr.res.i[!(is.na(tcr.res.i$TCR2)),]
        # select only TRB with top 
        tcr.res.i.trb <- tcr.res.i.trb[order(tcr.res.i.trb$umis, decreasing = TRUE),]
        tcr.res.i.trb <- tcr.res.i.trb[1,]

        Con.df[which(Con.df$barcode==barcode.i),"TCR2"] <- tcr.res.i.trb$TCR2
        Con.df[which(Con.df$barcode==barcode.i),"cdr3_aa2"] <- tcr.res.i.trb$cdr3
        Con.df[which(Con.df$barcode==barcode.i),"cdr3_nt2"] <- tcr.res.i.trb$cdr3_nt
    }
    return(Con.df)
}


calClonalFreq <- function(tcr.res, cloneType = "TCRgene") {
    stop("Function implementation has been masked")
}



TCRgeneCompMatrix <- function(tcr.barcode){
    Vgene <- c()
    Jgene <- c()
    for (i in seq_along(tcr.barcode$TCRgene)){
        TCRgene.i <- tcr.barcode$TCRgene[i]
        TCRgene.i.gene <- unlist(strsplit(TCRgene.i,split = "\\_|\\.|\\;"))
        TCRgene.i.Vgene <- TCRgene.i.gene[grepl(pattern = "^TRAV|^TRBV", TCRgene.i.gene)]
        TCRgene.i.Jgene <- TCRgene.i.gene[grepl(pattern = "^TRAJ|^TRBJ", TCRgene.i.gene)]
        
        Vgene <- c(Vgene, TCRgene.i.Vgene)
        Jgene <- c(Jgene, TCRgene.i.Jgene)
    }
    
    Vgene <- unique(Vgene)
    Jgene <- unique(Jgene)
    
    Vgene <- Vgene[order(nchar(Vgene), Vgene)]
    Jgene <- Jgene[order(nchar(Jgene), Jgene)]
    
    gene.matrix <- as.data.frame(matrix(data = 0,nrow = length(Jgene),
                                        ncol = length(Vgene)))
    colnames(gene.matrix) <- Vgene
    rownames(gene.matrix) <- Jgene
    
    for (i in seq_along(tcr.barcode$TCRgene)){
        TCRgene.i <- tcr.barcode$TCRgene[i]
        TRA.i <- unlist(strsplit(TCRgene.i,split = "_"))[1]
        TRB.i <- unlist(strsplit(TCRgene.i,split = "_"))[2]
        
        # for each TRA
        TRA.i.all <- unlist(strsplit(TRA.i, split = ";"))
        for (j in seq_along(TRA.i.all)){
            TRA.i.j <- TRA.i.all[j]
            TRA.i.j.all <- unlist(strsplit(TRA.i.j, split = "\\."))
            TRA.i.j.Vgene <- TRA.i.j.all[grepl(pattern = "^TRAV", x = TRA.i.j.all)]
            TRA.i.j.Jgene <- TRA.i.j.all[grepl(pattern = "^TRAJ", x = TRA.i.j.all)]
            gene.matrix[TRA.i.j.Jgene, TRA.i.j.Vgene] <- gene.matrix[TRA.i.j.Jgene, TRA.i.j.Vgene] + 1
        }
        
        # for each TRB
        TRB.i.all <- unlist(strsplit(TRB.i, split = ";"))
        for (j in seq_along(TRB.i.all)){
            TRB.i.j <- TRB.i.all[j]
            TRB.i.j.all <- unlist(strsplit(TRB.i.j, split = "\\."))
            TRB.i.j.Vgene <- TRB.i.j.all[grepl(pattern = "^TRBV", x = TRB.i.j.all)]
            TRB.i.j.Jgene <- TRB.i.j.all[grepl(pattern = "^TRBJ", x = TRB.i.j.all)]
            gene.matrix[TRB.i.j.Jgene, TRB.i.j.Vgene] <- gene.matrix[TRB.i.j.Jgene, TRB.i.j.Vgene] + 1
        }
        
    }
    
    return(gene.matrix)
}


getTCRCDR3fasta <- function(x){
    fasta.out <- c()
    for (i in 1:nrow(x)){
        x.i <- x[i,]
        barcode.i <- x.i[1,1]
        cdr3.i <- x.i[1,2]
        cdr3.i.all <- unlist(strsplit(cdr3.i, split = ";"))
        for (j in seq_along(cdr3.i.all)){
            barcode.i.j <- paste0(barcode.i,"-",j,split="")
            fasta.out <- c(fasta.out, paste0(">",barcode.i.j,""))
            fasta.out <- c(fasta.out, cdr3.i.all[j])
        }
    }
    return(fasta.out)
}


Complete the function implementation replacing "stop("Not implemented")".