assign.convergence: Check the convergence of the MCMC chain
In wevanjohnson/ASSIGN: Adaptive Signature Selection and InteGratioN (ASSIGN)

Description Usage Arguments Details Value Author(s) Examples

The assign.convergence checks the convergence of the MCMC chain of the model parameters generated by the Gibbs sampling algorithm.

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assign.convergence(test, burn_in = 0, iter = 2000, parameter = c("B", "S",
  "Delta", "beta", "kappa", "gamma", "sigma"), whichGene, whichSample,
  whichPath)

`test`	The list object returned from the assign.mcmc function. The list components are the MCMC chains of the B, S, Delta, beta, gamma, and sigma.
`burn_in`	The number of burn-in iterations. These iterations are discarded when computing the posterior means of the model parameters. The default is 0.
`iter`	The number of total iterations. The default is 2000.
`parameter`	A charater string indicating which model parameter is to be checked for convergency. This must be one of "B", "S", "Delta", "beta", "kappa", "gamma", and "sigma".
`whichGene`	A numerical value indicating which gene is to be checked for convergence. The value has to be in the range between 1 and G.
`whichSample`	A numerical value indicating which test sample is to be checked for convergence. The value has to be in the range between 1 and N.
`whichPath`	A numerical value indicating which pathway is to be checked for convergence. The value has to be in the range between 1 and K.

To compute the convergency of the gth gene in B, set whichGene=g, whichSample=NA, whichPath=NA.

To compute the convergency of the gth gene in the kth pathway within the signature matrix (S), set whichGene=g, whichSample=NA, whichPath=NA.

To compute the convergency of the kth pathway in the jth test sample within the pathway activation matrix (A), set whichGene=NA, whichSample=n, whichPath=k.

The assign.convergence function returns the a vector of the estimated values from each Gibbs sampling iteration of the model parameter to be checked, and a trace plot of this parameter.

Ying Shen

## Not run: 
# check the 10th gene in the 1st pathway for the convergency
trace.plot <- assign.convergence(test=mcmc.chain, burn_in=0, iter=2000, parameter="S", 
whichGene=10, whichSample=NA, whichPath=1)

## End(Not run)