flux.shape.from.one.point: Flux shape computing from one point

In SimEvolEnzCons: Simulation of Evolution of Enzyme Under Constraints

Description

flux.shape.from.one.point computes flux in every dimension (corresponding to each enzyme) from a given point (vector of concentrations)

Usage

flux.shape.from.one.point(Etot_fun, A_fun, correl_fun, beta_fun=NULL, 
E_ini_fun=NULL, from.eq=TRUE, E_fun=NULL, X_fun=1, with.alpha=FALSE, grp.reg=FALSE)

Arguments

Etot_fun	Numeric. The total concentration
A_fun	Numeric vector of activities
correl_fun	Character string indicating the abbreviation of the constraint applied on the system
beta_fun	Matrix of co-regulation coefficients
E_ini_fun	Numeric vector corresponding to initial concentrations.
from.eq	Logical. Is the analyzed point is the equilibrium point ? If TRUE, flux and selection coefficients are computed from the equilibrium, else E_fun is required. Default is TRUE.
E_fun	Numeric vector of the concentrations at analysed point. If from.eq=TRUE, E_fun is ignored.
X_fun	Numeric value. Default is 1
with.alpha	Logical. For case CR, is the computing method use alpha formula (TRUE) or pass by tau computing (FALSE) ?
grp.reg	Logical. Is there is some regulation groups in beta matrix ? If TRUE, tau will not be computed and give 0.

Details

Every enzyme correspond to one dimension in a n-dimensional graph.

From a given resident point E_fun, each value on dimension i is considered as a possible mutant of enzyme concentration E_i. Every "mutants" are taken between 0 and Etot_fun by 0.01 step. In every dimension, function flux.shape.from.one.point computes flux and selection coefficient (discrete coef_sel.discrete and continuous coef_sel.continue) from this point.

E_fun (resp. E_ini_fun) is rescaled by a cross product to have sum of E_fun (resp. E_ini_fun) equal to Etot_fun.

If from.eq=TRUE, analyzed point is:

• the theoretical equilibrium in case of independence "SC" and competition only "Comp";

• near the theoretical equilibrium (tau=0.95) in case of positive regulation only "RegPos" (due to infinite possible values for concentrations at this point);

• the effective equilibrium in other cases.

Default of E_ini_fun is NULL and corresponds to correl_fun equal to "SC" or "Comp", but in other cases (due to presence of regulation, E_ini_fun is obligatory and needs to have the same length as A_fun).

Value

Invisible list of 6 elements:

• $x : Numeric vector of all values that mutated enzymes can take, between 0 and Etot_fun, by 0.01. Length of (Etot_fun-0)*100.

• $J : Numeric matrix of n columns and (Etot_fun-0)*100 rows. Each column correspond to one direction (i.e. which enzyme is "mutated") and each row to each value of flux in this direction.

• $sel_disc : Numeric matrix corresponding to discrete selection coefficient. Same properties.

• $sel_cont : Numeric matrix corresponding to continuous selection coefficient. Same properties.

• $tau : Numeric matrix corresponding to position τ in case of regulation. Same properties.

• $param : List of input parameters

See Also

To understand differences between discrete and continuous selection coefficients, see function coef_sel.discrete and coef_sel.continue.

Examples

fsfop <- flux.shape.from.one.point(100,c(1,10,30),"SC")

SimEvolEnzCons documentation built on Oct. 29, 2021, 1:07 a.m.