defaultParams_student: Default Parameters for Linear Model with Student distributed...

In GRENITS: Gene Regulatory Network Inference Using Time Series

Description

Create parameter vector with default parameters for ReplicatesNet_student function

Usage

mcmc.defaultParams_student()

Details

Use this function to generate a template parameter vector to use non-default parameters for the ReplicatesNet_student model.

Value

Returns a single vector with the following elements (in this order):

(1) samples	Number of MCMC iterations to run
(2) burn.in	Number of initial iterations to discard as burn in
(3) thin	Subsampling frequency
(4) c	Shape parameter 1 for Beta(c,d) prior on rho (connectivity parameter)
(5) d	Shape parameter 2 for Beta(c,d) prior on rho (connectivity parameter)
(6) sigma.s	Standard deviation parameter for N(0,sigma.s) prior on B (Regression coefficients)
(7) a	Shape parameter for Gamma(a,b) prior on lambda (Regression precision)
(8) b	Rate parameter for Gamma(a,b) prior on lambda (Regression precision)
(9) a_exp	Shape parameter for Gamma(a_exp,b_exp) prior on tau (Replicates precision)
(10) b_exp	Rate parameter for Gamma(a_exp,b_exp) prior on tau (Replicates precision)
(11) a_deg	Shape parameter for Gamma(a_deg,b_deg) prior on nu (Student degrees of freedom)
(12) b_deg	Rate parameter for Gamma(a_deg,b_deg) prior on nu (Student degrees of freedom)
(13) sigma.mu	Standard deviation parameter for N(0,sigma.mu) prior on mu (Regression intercept)
(14) fix.y.iter	Number of iterations for which sampled data Y is fixed

References

Morrissey, E.R., Juarez, M.A., Denby, K.J. and Burroughs, N.J. 2010. On reverse engineering of gene interaction networks using time course data with repeated measurements. Bioinformatics 2010; doi: 10.1093/bioinformatics/btq421

See Also

plotPriors, ReplicatesNet_student.

Examples

    # Get default parameters
    linearNet_Student.params <- mcmc.defaultParams_student()

    # Change run length
    linearNet_Student.params[1] <- 200000

    # Change prior regression precision 
    linearNet_Student.params[7] <- 0.001
    linearNet_Student.params[8] <- 0.001

    # Plot to visualise changes
    plotPriors(linearNet_Student.params)

    ## Use to run ReplicatesNet_student ...

GRENITS documentation built on Nov. 8, 2020, 6:47 p.m.