Description Usage Arguments Details Value References See Also Examples
View source: R/coef_sel.continue.R
Computes the selection coefficient using the continuous expression s_i = R_i*δ_i/E_i
1 | coef_sel.continue(i_fun,E_res,A_fun,delta_fun,correl_fun,beta_fun=NULL)
|
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 |
correl_fun |
Character string indicating the abbreviation of the constraint applied on the system |
beta_fun |
Matrix of co-regulation coefficients |
Computes the selection coefficient using a continuous expression s_i = R_i*δ_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
.
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.
Coton et al. (2021)
Use function activities
to compute enzyme activities.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | #### 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)
|
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