SimEvolEnzCons (version 2.0.0)

coef_sel.continue: Selection coefficient computation

Description

Computes the selection coefficient using the continuous expression \(s_i = R_i*\delta_i/E_i\)

Usage

coef_sel.continue(i_fun,E_res,A_fun,delta_fun,correl_fun,beta_fun=NULL)

Arguments

i_fun

Integer number indicating the enzyme targeted by the mutation. See details

E_res

Numeric vector of resident enzyme concentrations

A_fun

Numeric vector of activities

delta_fun

Numeric. Actual effect of a mutation targeting enzyme i_fun, i.e. \(\delta_i\). See details

correl_fun

Character string indicating the abbreviation of the constraint applied on the system

beta_fun

Matrix of co-regulation coefficients

Value

Numeric value of the selection coefficient for the target enzyme.

If i_fun is set to 0, returns the numeric vector of the selection coefficients for the different enzyme.

Details

Computes the selection coefficient using a continuous expression \(s_i = R_i*\delta_i/E_i\)

Only mutations of concentrations are been considered.

i_fun is the number of the enzyme targeted by the mutation. It is an integer number between 0 and n, which is the total number of enzyme in the pathway. If i_fun is between 1 and n, delta_fun needs to be a single value and function coef_sel.continue computes the selection coefficient of a mutation of actual effect delta_fun targeting i_fun. If i_fun is set to 0, delta_fun needs to be a vector of same length as E_res. Each value of delta_fun is the actual effect of the mutation, and the position of this value in the vector is the target enzyme number. Thus, to see the effect of a mutation of given actual effect on every enzyme, set i_fun to 0 and delta_fun has to be a vector of same length as E_res.

References

Coton et al. (2021)

See Also

Use function activities to compute enzyme activities.

Examples

# NOT RUN {
#### Set
A <- c(1,10,30)
E <- c(30,30,30)
correl <- "CRPos"
beta <- matrix(c(1,10,5,0.1,1,0.5,0.2,2,1),nrow=3)
B <- apply(beta,1,sumbis)

### Mutation
mu <- 1
i <- 3
delta <- compute.delta(mu,E,correl,B)

#for enzyme i
coef_sel.continue(i,E,A,delta[i],correl,beta)

#for all enzyme
coef_sel.continue(0,E,A,delta,correl,beta)


# }