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This is an archived project. Repository and other project resources are read-only.
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general
ccb
sybil
Commits
107c64a7
Commit
107c64a7
authored
7 years ago
by
Claus Jonathan Fritzemeier
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replaced rBind and cBind with rbind and cbind
parent
65ce5eed
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4 changed files
DESCRIPTION
+4
-4
4 additions, 4 deletions
DESCRIPTION
R/addReact.R
+7
-7
7 additions, 7 deletions
R/addReact.R
R/doubleReact.R
+1
-1
1 addition, 1 deletion
R/doubleReact.R
R/sysBiolAlg_lmomaClass.R
+1
-1
1 addition, 1 deletion
R/sysBiolAlg_lmomaClass.R
with
13 additions
and
13 deletions
DESCRIPTION
+
4
−
4
View file @
107c64a7
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: 201
7
-0
7
-2
1
Date: 201
8
-0
3
-2
6
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: 201
7
-0
7
-2
1
12:34:14 UTC; jonathan
Packaged: 201
8
-0
3
-2
6
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],
...
...
This diff is collapsed.
Click to expand it.
R/addReact.R
+
7
−
7
View file @
107c64a7
...
@@ -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
::
rB
ind
(
newS
,
newRows
)
newS
<-
rb
ind
(
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
<-
c
B
ind
(
newS
,
rep
(
0
,
nrow
(
newS
)))
newS
<-
c
b
ind
(
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
<-
r
B
ind
(
ss
,
rep
(
FALSE
,
ncol
(
subSys
(
model
))))
newsubSys
<-
r
b
ind
(
ss
,
rep
(
FALSE
,
ncol
(
subSys
(
model
))))
}
}
}
}
else
{
else
{
if
(
is
(
subSystem
,
"logical"
))
{
if
(
is
(
subSystem
,
"logical"
))
{
newsubSys
<-
r
B
ind
(
subSys
(
model
),
subSystem
)
newsubSys
<-
r
b
ind
(
subSys
(
model
),
subSystem
)
}
}
else
{
else
{
nSubsRow
<-
colnames
(
subSys
(
model
))
%in%
subSystem
nSubsRow
<-
colnames
(
subSys
(
model
))
%in%
subSystem
newsubSys
<-
r
B
ind
(
subSys
(
model
),
nSubsRow
)
newsubSys
<-
r
b
ind
(
subSys
(
model
),
nSubsRow
)
}
}
}
}
# gpr association
# gpr association
if
(
ncol
(
rxnGeneMat
(
model
))
>
0
)
{
if
(
ncol
(
rxnGeneMat
(
model
))
>
0
)
{
newrxnGeneMat
<-
r
B
ind
(
rxnGeneMat
(
model
),
newrxnGeneMat
<-
r
b
ind
(
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
<-
c
B
ind
(
newrxnGeneMat
,
newrxnGeneMat
<-
c
b
ind
(
newrxnGeneMat
,
rep
(
FALSE
,
nrow
(
newrxnGeneMat
)))
rep
(
FALSE
,
nrow
(
newrxnGeneMat
)))
}
}
}
}
...
...
This diff is collapsed.
Click to expand it.
R/doubleReact.R
+
1
−
1
View file @
107c64a7
...
@@ -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
<-
c
B
ind
(
S
(
model
)[,
columns
[[
i
]]
])
Stmp
<-
c
b
ind
(
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
...
...
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Click to expand it.
R/sysBiolAlg_lmomaClass.R
+
1
−
1
View file @
107c64a7
...
@@ -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
<-
r
B
ind
(
LHSwt
,
LHS
,
crow
)
LHS
<-
r
b
ind
(
LHSwt
,
LHS
,
crow
)
subalg
<-
"lmoma_cobra"
subalg
<-
"lmoma_cobra"
}
}
...
...
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