R/generateFluxdels.R

In sybil: Efficient Constrained Based Modelling

#  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))

}