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# 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)
}
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