R/build_ParameterMatrix.R

In alessandrozito/BayesANT: Bayesian Nonparametric Taxonomic classifier

build_ParameterMatrix <- function(nodes, Nucl_counts, hyperparameters) {
  M <- matrix(0, nrow = length(nodes), ncol = length(Nucl_counts[[1]]))

  for (i in 1:length(nodes)) {
    index_phy <- which(names(Nucl_counts) == nodes[i])
    index_prior <- which(names(hyperparameters) == nodes[i])

    if (grepl("_new$", nodes[i])) {
      m1 <- hyperparameters[[index_prior]]
    } else {
      m1 <- hyperparameters[[index_prior]] + Nucl_counts[[index_phy]]
    }
    M[i, ] <- c(t(t(m1) / colSums(m1)))
  }
  return(M)
}

build_ParameterMatrix_from_Kmers <- function(nodes, Kmer_counts, hyperparameters) {
  K <- matrix(0, nrow = length(nodes), ncol = ncol(Kmer_counts[[1]]$Kmers))

  for (i in 1:length(nodes)) {
    index_phy <- which(names(Kmer_counts) == nodes[i])
    index_prior <- which(names(hyperparameters) == nodes[i])

    if (grepl("_new$", nodes[i])) {
      m1 <- hyperparameters[[index_prior]]
    } else {
      m1 <- hyperparameters[[index_prior]] + colSums(Kmer_counts[[index_phy]]$Kmers)
    }
    K[i, ] <- m1
  }
  return(K)
}