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sybilSBML.R

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    generateFluxdels.R 1.53 KiB
    #  generateFluxdels.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: .generateFluxdels
    #
    #
    #
    
    .generateFluxdels <- function(model, geneList) {
    
        message("compute affected fluxes ... ", appendLF = FALSE)
        
        react <- mapply(geneDel, geneList,
                        MoreArgs = list(model = model), SIMPLIFY = FALSE)
    #    react <- as.list(1:length(geneList))
        heff  <- ! sapply(react, is.null, simplify = TRUE, USE.NAMES = FALSE)
    
        fd       <- vector(mode = "list", length = length(react))
        fd[heff] <- lapply(react[heff], function(x) react_id(model)[x])
    
        message("OK")
    
        return(list(react = react, heff = heff, fd = fd))
    
    }