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prepareSubSysMatrix.R

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    Claus Jonathan Fritzemeier authored
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    prepareSubSysMatrix.R 1.95 KiB
    #  prepareSubSysMatrix.R
    #  FBA and friends with R.
    #
    #  Copyright (C) 2010-2014 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
    #  Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
    #  All right reserved.
    #  Email: geliudie@uni-duesseldorf.de
    #
    #  This file is part of sybil.
    #
    #  Sybil 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 3 of the License, or
    #  (at your option) any later version.
    #
    #  Sybil 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.
    #
    #  You should have received a copy of the GNU General Public License
    #  along with sybil.  If not, see <http://www.gnu.org/licenses/>.
    
    
    ################################################
    # Function: .prepareSubSysMatrix
    #
    #
    #
    
    .prepareSubSysMatrix <- function(reactSUBS, nreact, entrydelim = NA) {
    
        if (!is.null(reactSUBS)) {
    
            reactSsys <- as.character(reactSUBS)
    
            ssys_tmp <- strsplit(reactSsys, entrydelim, fixed = TRUE)
    
            sys_names <- unique(unlist(ssys_tmp))
            ssys <- Matrix::Matrix(FALSE,
                                   nrow = length(reactSUBS),
                                   ncol = length(sys_names),
                                   sparse = TRUE)
    
            colnames(ssys) <- sys_names
    
            ssys_id <- mapply(match,
                              ssys_tmp,
                              MoreArgs = list(sys_names),
                              SIMPLIFY = FALSE)
    
            for (i in seq(along = ssys_id)) {
                if (length(ssys_id[[i]]) > 0) {
                    ssys[i, ssys_id[[i]]] <- TRUE
                }
            }
    
        }
        else {
            ssys <- Matrix::Matrix(FALSE, nrow = nreact, ncol = 1, sparse = TRUE)
            colnames(ssys) <- NA
        }
    
        return(ssys)
    
    }