R/build_CountMatrix.R

In alessandrozito/BayesANT: Bayesian Nonparametric Taxonomic classifier

build_CountMatrix <- function(seqDNA_mat, nucl = c("-", "A", "C", "G", "T"), case_upper = TRUE) {
  if (case_upper == FALSE) {
    nucl <- tolower(nucl)
  }
  CountMatrix <- matrix(NA, nrow = length(nucl), ncol = ncol(seqDNA_mat))
  for (d in 1:length(nucl)) {
    CountMatrix[d, ] <- colSums(seqDNA_mat == nucl[d])
  }
  return(CountMatrix)
}