R/distanceMatrix.r

In chasemc/ghosts: Protein and small molecule analysis of bacteria by MALDI-TOF MS

#' Create Distance Matrix
#'
#' @param data matrix or dataframe, where columns are variables and rows are samples
#' @param method distance metric to use
#' @param booled whether all values >0 should be set to one
#'
#' @return distance matrix
#' @export

distMatrix <- function(data,
                       method,
                       booled){
   validate(need(nrow(data) > 2, "Need >2 samples to cluster")) 
   data <- base::as.matrix(data)
  # Change empty to 0
   data[base::is.na(data)] <- 0
   data[base::is.null(data)] <- 0
   
   if (booled == "TRUE") {
     data[data > 0] <- 1
   }
  
  if (method == "cosine") {
    return(stats::as.dist(1 - coop::tcosine(data)))
  }else{
    return(stats::dist(data, method = method))
  }
}