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Commit 107c64a7 authored by Claus Jonathan Fritzemeier's avatar Claus Jonathan Fritzemeier
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replaced rBind and cBind with rbind and cbind

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Package: sybil Package: sybil
Type: Package Type: Package
Title: Efficient Constrained Based Modelling in R Title: Efficient Constrained Based Modelling in R
Version: 2.1.0 Version: 2.1.1
Date: 2017-07-21 Date: 2018-03-26
Authors@R: c( Authors@R: c(
person(c("C.", "Jonathan"), "Fritzemeier", role = c("cre", "ctb"), email = "clausjonathan.fritzemeier@uni-duesseldorf.de"), person(c("C.", "Jonathan"), "Fritzemeier", role = c("cre", "ctb"), email = "clausjonathan.fritzemeier@uni-duesseldorf.de"),
person("Gabriel", "Gelius-Dietrich", role = c("aut")), person("Gabriel", "Gelius-Dietrich", role = c("aut")),
...@@ -12,7 +12,7 @@ Authors@R: c( ...@@ -12,7 +12,7 @@ Authors@R: c(
person("Abdelmoneim", "Desouki", role = "ctb"), person("Abdelmoneim", "Desouki", role = "ctb"),
person(c("Martin", "J."), "Lercher", role = "ctb")) person(c("Martin", "J."), "Lercher", role = "ctb"))
Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de> Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
Depends: R (>= 2.14.2), Matrix, lattice Depends: R (>= 3.2.0), Matrix, lattice
Imports: methods Imports: methods
Suggests: glpkAPI (>= 1.2.8), cplexAPI (>= 1.2.4), clpAPI (>= 1.2.4), Suggests: glpkAPI (>= 1.2.8), cplexAPI (>= 1.2.4), clpAPI (>= 1.2.4),
lpSolveAPI (>= 5.5.2.0), parallel, grid lpSolveAPI (>= 5.5.2.0), parallel, grid
...@@ -55,7 +55,7 @@ Collate: generics.R validmodelorg.R validoptsol.R validreactId.R validreact.R ...@@ -55,7 +55,7 @@ Collate: generics.R validmodelorg.R validoptsol.R validreactId.R validreact.R
sysBiolAlg_mtfClass.R sysBiolAlg_mtfEasyConstraintClass.R sysBiolAlg_mtfClass.R sysBiolAlg_mtfEasyConstraintClass.R
sysBiolAlg_roomClass.R sybilLogClass.R upgradeModelorg.R sysBiolAlg_roomClass.R sybilLogClass.R upgradeModelorg.R
mergeReact2Modelorg.R mergeReact2Modelorg.R
Packaged: 2017-07-21 12:34:14 UTC; jonathan Packaged: 2018-03-26 12:34:14 UTC; jonathan
Author: C. Jonathan Fritzemeier [cre, ctb], Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut], Gabriel Gelius-Dietrich [aut],
Rajen Piernikarczyk [ctb], Rajen Piernikarczyk [ctb],
......
...@@ -186,7 +186,7 @@ setMethod("addReact", signature(model = "modelorg"), ...@@ -186,7 +186,7 @@ setMethod("addReact", signature(model = "modelorg"),
newRows <- Matrix::Matrix(0, newRows <- Matrix::Matrix(0,
nrow = nNewRows, nrow = nNewRows,
ncol = react_num(model)) ncol = react_num(model))
newS <- Matrix::rBind(newS, newRows) newS <- rbind(newS, newRows)
# new met attrs # new met attrs
if(ncol(newMetAttr) > 0){ if(ncol(newMetAttr) > 0){
...@@ -220,7 +220,7 @@ setMethod("addReact", signature(model = "modelorg"), ...@@ -220,7 +220,7 @@ setMethod("addReact", signature(model = "modelorg"),
newobj_coef <- append(obj_coef(model), obj) newobj_coef <- append(obj_coef(model), obj)
# new column in stoichiometric matrix # new column in stoichiometric matrix
newS <- cBind(newS, rep(0, nrow(newS))) newS <- cbind(newS, rep(0, nrow(newS)))
# new react Attr # new react Attr
# only one new row, /bc we can only add one reaction a time. # only one new row, /bc we can only add one reaction a time.
...@@ -236,23 +236,23 @@ setMethod("addReact", signature(model = "modelorg"), ...@@ -236,23 +236,23 @@ setMethod("addReact", signature(model = "modelorg"),
newsubSys <- ss newsubSys <- ss
} }
else { else {
newsubSys <- rBind(ss, rep(FALSE, ncol(subSys(model)))) newsubSys <- rbind(ss, rep(FALSE, ncol(subSys(model))))
} }
} }
else { else {
if (is(subSystem, "logical")) { if (is(subSystem, "logical")) {
newsubSys <- rBind(subSys(model), subSystem) newsubSys <- rbind(subSys(model), subSystem)
} }
else { else {
nSubsRow <- colnames(subSys(model)) %in% subSystem nSubsRow <- colnames(subSys(model)) %in% subSystem
newsubSys <- rBind(subSys(model), nSubsRow) newsubSys <- rbind(subSys(model), nSubsRow)
} }
} }
# gpr association # gpr association
if (ncol(rxnGeneMat(model)) > 0) { if (ncol(rxnGeneMat(model)) > 0) {
newrxnGeneMat <- rBind(rxnGeneMat(model), newrxnGeneMat <- rbind(rxnGeneMat(model),
rep(FALSE, ncol(rxnGeneMat(model)))) rep(FALSE, ncol(rxnGeneMat(model))))
} }
else { #if (nrow(rxnGeneMat(model)) > 0) { else { #if (nrow(rxnGeneMat(model)) > 0) {
...@@ -294,7 +294,7 @@ setMethod("addReact", signature(model = "modelorg"), ...@@ -294,7 +294,7 @@ setMethod("addReact", signature(model = "modelorg"),
} }
else { else {
for (i in seq(along = gene_rule[["gene"]][new_gene])) { for (i in seq(along = gene_rule[["gene"]][new_gene])) {
newrxnGeneMat <- cBind(newrxnGeneMat, newrxnGeneMat <- cbind(newrxnGeneMat,
rep(FALSE, nrow(newrxnGeneMat))) rep(FALSE, nrow(newrxnGeneMat)))
} }
} }
......
...@@ -123,7 +123,7 @@ doubleReact <- function(model, checkRev = TRUE, linInd = FALSE) { ...@@ -123,7 +123,7 @@ doubleReact <- function(model, checkRev = TRUE, linInd = FALSE) {
# Put the columns of S into a new matrix, which contain the same # Put the columns of S into a new matrix, which contain the same
# number of metabolites # number of metabolites
Stmp <- cBind(S(model)[, columns[[i]] ]) Stmp <- cbind(S(model)[, columns[[i]] ])
# translate Stmp into a matrix with the row indices of the # translate Stmp into a matrix with the row indices of the
# non zero elements # non zero elements
......
...@@ -154,7 +154,7 @@ setMethod(f = "initialize", ...@@ -154,7 +154,7 @@ setMethod(f = "initialize",
sparse = TRUE) sparse = TRUE)
# the final contraint matrix # the final contraint matrix
LHS <- rBind(LHSwt, LHS, crow) LHS <- rbind(LHSwt, LHS, crow)
subalg <- "lmoma_cobra" subalg <- "lmoma_cobra"
} }
......
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