addExchReact: Add Exchange Reactions to a Model

In sybil: Efficient Constrained Based Modelling

Description

The function addExchReact adds exchange reactions for a set of metabolites to a metabolic model.

Usage

  addExchReact(model, met, lb, ub)

Arguments

model	An object of class modelorg.
met	A vector of character strings containing the metabolite id's to add exchange reactions for.
lb	A vector of numeric values of the same length as met containing the lower bounds for the exchange reactions. Default: rep(0, length(met)).
ub	A vector of numeric values of the same length as met containing the upper bounds for the exchange reactions. Default: rep(SYBIL_SETTINGS("MAXIMUM"), length(met)).

Details

If lb[i] < 0, the exchange reaction for the metabolite in met[i] is considered to be reversible, otherwise irreversible. A reaction id is generated for each exchange reaction by prepending the metabolite id's with the string "Ex_".

Value

An object of class modelorg

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

References

Becker, S. A., Feist, A. M., Mo, M. L., Hannum, G., Palsson, B. Ø. and Herrgard, M. J. (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2, 727–738.

Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., Kang, J., Hyduke, D. R. and Palsson, B. Ø. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6, 1290–1307.

See Also

modelorg and addReact

Examples

  # add exchange reactions (allowing input) for the metabolites
  # malate and oxalacetate
  data(Ec_core)
  mod <- addExchReact(Ec_core,
                      met = c("mal_L[c]", "oaa[c]"),
                      lb = c(-20, -20))
  findExchReact(mod)

Example output

Loading required package: Matrix
Loading required package: lattice
Warning messages:
1: 'cBind' is deprecated.
 Since R version 3.2.0, base's cbind() should work fine with S4 objects 
2: 'rBind' is deprecated.
 Since R version 3.2.0, base's rbind() should work fine with S4 objects 
  #   pos.  reaction id           metabolite id          uptake     lb     ub
 [1]  20    EX_ac(e)              ac[e]                  FALSE       0    Inf
 [2]  21    EX_acald(e)           acald[e]               FALSE       0    Inf
 [3]  22    EX_akg(e)             akg[e]                 FALSE       0    Inf
 [4]  23    EX_co2(e)             co2[e]                 TRUE     -Inf    Inf
 [5]  24    EX_etoh(e)            etoh[e]                FALSE       0    Inf
 [6]  25    EX_for(e)             for[e]                 FALSE       0    Inf
 [7]  26    EX_fru(e)             fru[e]                 FALSE       0    Inf
 [8]  27    EX_fum(e)             fum[e]                 FALSE       0    Inf
 [9]  28    EX_glc(e)             glc_D[e]               TRUE      -10    Inf
[10]  29    EX_gln_L(e)           gln_L[e]               FALSE       0    Inf
[11]  30    EX_glu_L(e)           glu_L[e]               FALSE       0    Inf
[12]  31    EX_h(e)               h[e]                   TRUE     -Inf    Inf
[13]  32    EX_h2o(e)             h2o[e]                 TRUE     -Inf    Inf
[14]  33    EX_lac_D(e)           lac_D[e]               FALSE       0    Inf
[15]  34    EX_mal_L(e)           mal_L[e]               FALSE       0    Inf
[16]  35    EX_nh4(e)             nh4[e]                 TRUE     -Inf    Inf
[17]  36    EX_o2(e)              o2[e]                  TRUE     -Inf    Inf
[18]  37    EX_pi(e)              pi[e]                  TRUE     -Inf    Inf
[19]  38    EX_pyr(e)             pyr[e]                 FALSE       0    Inf
[20]  39    EX_succ(e)            succ[e]                FALSE       0    Inf
[21]  96    Ex_mal_L[c]           mal_L[c]               TRUE      -20    Inf
[22]  97    Ex_oaa[c]             oaa[c]                 TRUE      -20    Inf

number of exchange reactions: 22

sybil documentation built on May 31, 2021, 5:08 p.m.