SIfEK (version 0.1.0)

DA.MM: Estimation of single Michaelis-Menten constant using diffusion approximation

Description

The function estimates single Michaelis-Menten constant using the likelihood function with diffusion approximation method.

Usage

DA.MM(method = T, dat, enz, subs, MM, catal, nrepeat = 10000,
  jump = 1, burning = 0, MM_m_v = c(1, 10000), sig, scale_tun = 80)

Arguments

method

method selection: T=TQ model, F=SQ model(default = T)

dat

observed dataset ( time & trajectory columns)

enz

enzyme concentrate

subs

substrate concentrate

MM

initial value of MM constant

catal

true value of catalytic constant

nrepeat

total number of iteration (default=10000)

jump

length of distance (default = 1)

burning

length of burning period (default=0)

MM_m_v

MM prior gamma mean, variance(default=c(1,10000))

sig

standard deviation of univariate Normal proposal distribution

scale_tun

scale tunning constant for stochastic simulation

Value

A vector of posterior samples of catalytic constant

Details

The function DA.MM generates a set of MCMC simulation samples from the conditional posterior distribution of Michaelis-Menten constant of enzyme kinetics model. As the MM constant is only parameter to be estimated in the function the user should assign catalytic constant as well as initial enzyme concentration and substrate concentration. The prior information for the parameter can be given. The turning constant (scale_tun) and standard deviation (sig) can be set to controlled proper mixing and acceptance ratio of the parameter from the conditional posterior distribution. The posterior samples are only stored with fixed interval according to set "jump" to reduce serial correlation. The initial iterations are removed for convergence. The <U+201C>burning<U+201D> is set the length of initial iterations. The diffusion approximation method is used for construction of the likelihood.

Examples

# NOT RUN {
data('Chymo_low')
sm_DA=DA.MM(method=TRUE,dat=Chymo_low,enz=4.4e+7,subs = 4.4e+7,MM=4.4e+8,catal=0.05
                  ,nrepeat=10000,jump=1,burning = 0,MM_m_v=c(1,1e+10),sig=500)
# }
# NOT RUN {
# }