R/compute_pbem_allele.R

In abemus: Adaptive Base Error Model in Ultra-Deep Sequencing Data

compute_pbem_allele <- function(id,abemus){
  locus = abemus[id,,drop=FALSE]
  locus$pbem_allele = as.numeric(locus[paste0('total.',locus$alt)]/locus$tot_coverage)
  # check if same alt allele is observed in case and germline (when af germline > 0)
  alt_case = as.numeric(locus[paste0(locus$alt,'_case')])
  alt_ctrl = as.numeric(locus[paste0(locus$alt,'_control')])
  if(is.na(alt_ctrl)){
    locus$same_allele = NA
  } else {
    if(alt_ctrl>0){
      locus$same_allele = 1
    } else {
      locus$same_allele = 0
    }
  }
  return(locus)
}