R/check.matrix.R

In antagomir/netresponse: Functional Network Analysis

# Copyright (C) 2008-2012 Olli-Pekka Huovilainen and Leo Lahti Contact: Leo Lahti
# <leo.lahti@iki.fi> This program is free software; you can redistribute it
# and/or modify it under the terms of the GNU General Public License as published
# by the Free Software Foundation; either version 2, or (at your option) any
# later version.  This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for
# more details.

# The best academic advice I ever got was: 'Spend at least an hour every day on
# the manuscript closest to publication'.

#' check.matrix
#' 
#' Mostly for internal purposes. Check input matrix format.
#' 
#' 
#' @usage check.matrix(datamatrix)
#' @param datamatrix See detect.responses
#' @return The datamatrix, possibly added with necessary formatting for the
#' netresponse algorithm.
#' @author Leo Lahti, Olli-Pekka Huovilainen and Antonio Gusmao.  Maintainer:
#' Leo Lahti \email{leo.lahti@@iki.fi}
#' @seealso detect.responses
#' @references See citation('netresponse')
#' @keywords internal
#' @examples # datamatrix <- check.matrix(datamatrix)
check.matrix <- function(datamatrix) {
    
    accepted.formats.emat <- c("matrix", "Matrix", "data.frame")
    
    # ensure datamatrix is a matrix
    if (!is.matrix(datamatrix)) {
        if (class(datamatrix) %in% accepted.formats.emat) {
            datamatrix <- as.matrix(datamatrix)
        } else {
            stop(paste("datamatrix needs to be in one of the following formats:", 
                paste(accepted.formats.emat, collapse = "; ")))
        }
    }
    if (is.null(colnames(datamatrix))) {
        colnames(datamatrix) <- as.character(seq_len(ncol(datamatrix)))
    }
    if (is.null(rownames(datamatrix))) {
        rownames(datamatrix) <- as.character(seq_len(nrow(datamatrix)))
    }
    
    datamatrix
}