R/dec2bin.R

In chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

#' Conversion of decimal and binary states
#'
#' Convert combinatorial states in decimal representation to combinatorial states in binary representation and vice versa.
#'
#' \pkg{\link{chromstaR}} uses decimal numbers to represent combinatorial states of peaks. These functions serve as a convenient way to get from the efficient decimal representation to a more human-readable binary representation.
#' @return A vector of integers for \code{bin2dec} and a matrix of logicals with one state per row for \code{dec2bin}.
#' @examples
#'decimal.states <- c(0:31)
#'binary.states <- dec2bin(decimal.states, colnames=paste0('mark',1:5))
#'control.decimal.states <- bin2dec(binary.states)
#' @name conversion
NULL

#' @describeIn conversion Decimal to binary conversion.
#' @param dec A vector with whole numbers.
#' @param colnames The column names for the returned matrix. If specified, \code{ndigits} will be the length of \code{colnames}.
#' @param ndigits The number of digits that the binary representation should have. If unspecified, the shortest possible representation will be chosen.
#' @author Aaron Taudt
#' @export
dec2bin = function(dec, colnames=NULL, ndigits=NULL) {

    # Check user input
    dec <- as.numeric(as.character(dec))
    maxdec = max(dec)
    if (!is.null(colnames)) {
        ndigits <- length(colnames)
    } else {
        if (!is.null(ndigits)) {
            if (check.positive.integer(ndigits)!=0) stop("argument 'ndigits' expects a positive integer")
        }
    }
    
    modulos <- list()
    mod <- 1
    dectemp <- dec
    while (any(dectemp!=0)) {
        mod <- as.logical(dectemp %% 2)
        modulos[[length(modulos)+1]] <- mod
        dectemp <- dectemp %/% 2
    }
    
    if (is.null(ndigits)) {
        ndigits <- max(length(modulos),1)
    }
    binary.states <- matrix(FALSE, nrow=length(dec), ncol=ndigits)
    if (length(modulos)>0) {
        for (i1 in 1:min(length(modulos), ndigits)) {
            binary.states[ ,ncol(binary.states)+1-i1] <- modulos[[i1]]
        }
    }
    if (!is(binary.states, 'matrix')) {
        binary.states <- matrix(binary.states, nrow=length(dec))
    }

    colnames(binary.states) <- colnames
    rownames(binary.states) <- dec
    mode(binary.states) <- 'logical'
    return(binary.states)

}

#' @describeIn conversion Binary to decimal conversion.
#' @param bin A matrix with only 0 and 1 (or TRUE and FALSE) as entries. One combinatorial state per row.
#' @export
bin2dec = function(bin) {
    if (!is.matrix(bin)) {
        bin <- matrix(bin, nrow=1)
        warning("Argument 'bin' is not a matrix. Interpreting 'bin' as matrix with one row.")
    }
    dec = rep(0,nrow(bin))
    for (i1 in 1:ncol(bin)) {
        dec = dec + 2^(ncol(bin)-i1) * bin[,i1]
    }
    return(dec)
}