R/chromR_to_vcfR.R

In knausb/vcfR: Manipulate and Visualize VCF Data

#' @title Convert chrom objects to vcfR objects
#' @rdname chrom_to_vcfR
#' @export
#'
#' @description
#' Convert chrom objects to vcfR objects.
#'
#' @param x Object of class chrom
#' @param use.mask Logical, determine if mask from chrom object should be used to subset vcf data
#'
#' @details
#' The chrom object is subset and recast as a vcfR object.  When use.mask is set 
#' to TRUE (the default), the object is subset to only the variants (rows) indicated
#' to include by the mask.  When use.mask is set to FALSE, all variants (rows) from 
#' the chrom object are included in the new vcfR object.
#' 
#' @return Returns an object of class vcfR. 
#' 
#'
chromR2vcfR <- function(x, use.mask=FALSE){
#  if(class(x) != "chromR"){
  if( !inherits(x, "chromR") ){
    stop("Unexpected class! Expecting an object of class chromR.")
  }
  mask <- x@var.info$mask
  vcf <- x@vcf
  
  if(use.mask == TRUE){
    vcf <- vcf[mask,]
  }

  return(vcf)
}