R/addID.R

In vcfR: Manipulate and Visualize VCF Data

#' @title Populate the ID column of VCF data
#' @name addID
#' @rdname addID
#' 
#' @description
#' Populate the ID column of VCF data by concatenating the chromosome, position and optionally an index. 
#'  
#' @param x an object of class vcfR or chromR.
#' @param sep a character string to separate the terms.
#' 
#' @details 
#' Variant callers typically leave the ID column empty in VCF data.
#' However, the VCF data may potentially include variants with IDs as well as variants without.
#' This function populates the missing elements by concatenating the chromosome and position.
#' When this concatenation results in non-unique names, an index is added to force uniqueness.
#' 
#' 
#' @examples
#' data(vcfR_test)
#' head(vcfR_test)
#' vcfR_test <- addID(vcfR_test)
#' head(vcfR_test)
#' 
#' 
#' @export
#' 
addID <- function(x, sep="_"){
#  if( class(x) == 'chromR' ){
  if( inherits(x, "chromR") ){
    ID <- x@vcf@fix[,'ID']
    CHROM <- x@vcf@fix[,'CHROM']
    POS <- x@vcf@fix[,'POS']
#  } else if( class(x) == 'vcfR' ){
  } else if( inherits(x,'vcfR') ){
    ID <- x@fix[,'ID']
    CHROM <- x@fix[,'CHROM']
    POS <- x@fix[,'POS']
  } else {
    stop("expecting an object of class vcfR or chromR.")
  }
  
  if( sum(!is.na(ID)) < length(ID) ){
    ID[ is.na(ID) ] <- paste( CHROM[ is.na(ID) ], POS[ is.na(ID) ], sep=sep )
    if( length(unique(ID)) < length(ID) ){
      ID <- paste( ID, 1:length(ID), sep=sep )
    }
  }
  
#  if( class(x) == 'chromR' ){
  if( inherits(x, 'chromR') ){
    x@vcf@fix[,'ID'] <- ID
#  } else if( class(x) == 'vcfR' ){
  } else if( inherits(x, 'vcfR') ){
    x@fix[,'ID'] <- ID
  } else {
    stop("expecting an object of class vcfR or chromR.")
  }
  
  return(x)
}