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# recodeMatrix.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: .recodeMatrix
#
# arguments:
#
# mat: the matrix to recode (class Matrix)
# signs: character vector of length three:
# mat[i, j] > tol --> signs[3]
# mat[i, j] < tol --> signs[1]
# mat[i, j] == tol --> signs[2]
# tol: tolerance value
.recodeMatrix <- function(mat,
signs = c("-", " ", "+"),
tol = SYBIL_SETTINGS("TOLERANCE")) {
stopifnot(is(mat, "Matrix"), length(signs) == 3)
mat <- apply(mat, 2,
function(x) {
ifelse(x > tol, signs[3], ifelse(abs(x) > tol,
signs[1], signs[2]))
})
return(mat)
}
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