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

In SIfEK: Statistical Inference for Enzyme Kinetics

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

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 “burning” is set the length of initial iterations. The diffusion approximation method is used for construction of the likelihood.

Value

A vector of posterior samples of catalytic constant

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)

## End(Not run)

SIfEK documentation built on May 1, 2019, 9:11 p.m.