HITChipDB: HITChipDB

#' Description: Write matrix in tab file
#'
#' @param dat data matrix
#' @param filename output file
#' @param verbose verbose
#' @return output file location
#'
#' @export
#' @references See citation("microbiome") 
#' @author Contact: Leo Lahti \email{microbiome-admin@@googlegroups.com}
#' @keywords utilities
WriteMatrix <- function (dat, filename, verbose = FALSE) { 

  if (verbose) { message(paste("Writing output in ", filename)) }
  write.table(dat, file = filename, quote = FALSE, sep = "\t", row.names = FALSE)
  filename

}


#' Description: determine threshold for bg correction
#'
#' Arguments:
#' @param dat data matrix (in approximately normal scale ie. logged)
#'
#' Returns:
#' @return threshold value
#'
#' @export
#' @references See citation("microbiome") 
#' @author Contact: Leo Lahti \email{microbiome-admin@@googlegroups.com}
#' @keywords utilities

estimate.min.threshold <- function (dat) {

  #estimate min threshold 
  DD <- density(as.numeric(unlist(dat)))

  #find mode
  noise_mode <- DD$x[[which.max(DD$y)]] # DD$x[which(diff(DD$y)<0)[1]]

  #compute sd of noise
  noise_sd <- sd(dat[dat < noise_mode])

  #threshold
  low.thresh <- noise_mode + 6*noise_sd

  low.thresh
}