phpp: Phenotypic Phase Plane Analysis

In sybil: Efficient Constrained Based Modelling

Description

Performs phenotypic phase plane analysis for a given metabolic model.

Usage

phpp(model, ctrlreact, rng = c(0, 0, 20, 20),
     numP = 50, setToZero = TRUE, redCosts = FALSE, ...)

Arguments

model	An object of class modelorg.
ctrlreact	An object of class reactId, character or integer. Specifies two control reactions.
rng	A numeric vector of length four, giving the lower and upper bounds of the control reactions. The first two values contain the lower bounds, the last two values the upper bounds. Default: c(0, 0, 20, 20)
numP	The number of points to analyse. Default: 50
setToZero	Logical: If the mathematical programming software returns a solution status which is not optimal, set the corresponding objective value to zero (see also optimizer). Default: TRUE.
redCosts	Logical: store reduced costs of the control variables. Default: FALSE.
...	Further arguments passed to optimizer.

Details

The two control reactions given in argument ctrlreact are treated as uptake reactions: reactions that transport metabolites into the metabolic network. That means, the optimizations are performed using abs(rng) * -1.

Value

An object of class optsol_phpp.

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.

Edwards, J. S., Ibarra, R. U. and Palsson, B. Ø. (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19, 125–130.

Edwards, J. S., Ramakrishna, R. and Palsson, B. Ø. (2002) Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnol Bioeng 77, 27–36.

Bernhard Ø. Palsson (2006). Systems Biology: Properties of Reconstructed Networks. Cambridge University Press.

Examples

  data(Ec_core)
  
  # switch off glucose input
  Ec_core_wo_glc <- changeUptake(Ec_core, off = "glc_D[e]")
  opt <- phpp(Ec_core_wo_glc, ctrlreact = c("EX_succ(e)", "EX_o2(e)"))
  
  # plot phenotypic phase plane
  plot(opt)
  
  # plot reduced costs of the two control reactions
  plot(opt, "EX_succ(e)")
  plot(opt, "EX_o2(e)")

Example output

Loading required package: Matrix
Loading required package: lattice
Loading required package: glpkAPI
using GLPK version 4.65
calculating 2500 optimizations ... 
|            :            |            :            | 100 %
|===================================================| :-) 
OK
setting 1075 objective values to zero
Done.
[1] NA
Warning message:
In .local(x, y, ...) : solution object does not contain reduced costs
[1] NA
Warning message:
In .local(x, y, ...) : solution object does not contain reduced costs

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