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# 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))
}
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