calculateDistanceMatrix.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/distances_and_export.R
\name{calculateDistanceMatrix}
\alias{calculateDistanceMatrix}
\title{Calculate pairwise distance matrix for multiple sequences}
\usage{
calculateDistanceMatrix(freq_matrices, distance_type = "Euclidean")
}
\arguments{
\item{freq_matrices}{List. A named list of frequency matrices, one per
sequence, as returned by cgat().}

\item{distance_type}{Character. Type of distance to calculate:
"Euclidean" (default), "S_Euclidean", or "Manhattan".}
}
\value{
Numeric matrix. A symmetric distance matrix with sequence names as
  row and column names.
}
\description{
Computes a full pairwise distance matrix from a list of CGR frequency
matrices.
}
\details{
This function calculates all pairwise distances between sequences based on
their CGR frequency matrices. The resulting distance matrix can be used for
phylogenetic tree construction, clustering, or other downstream analyses.
}
\examples{
# Build two minimal frequency matrices (4 k-mers each, normalized)
fm1 <- matrix(c(0.4, 0.3, 0.2, 0.1), ncol = 1,
              dimnames = list(c("A", "C", "G", "T"), NULL))
fm2 <- matrix(c(0.1, 0.2, 0.3, 0.4), ncol = 1,
              dimnames = list(c("A", "C", "G", "T"), NULL))
fm3 <- matrix(c(0.25, 0.25, 0.25, 0.25), ncol = 1,
              dimnames = list(c("A", "C", "G", "T"), NULL))

freq_list <- list(Seq1 = fm1, Seq2 = fm2, Seq3 = fm3)

dist_matrix <- calculateDistanceMatrix(freq_list, distance_type = "Euclidean")
print(round(dist_matrix, 4))

}