ccParams {BGmix}R Documentation

Read posterior means and classification probabilities from BGmix

Description

Reads output files containing posterior means from BGmix AND reads posterior probabilities of each gene being classified in the null mixture component.

Usage

ccParams(filedir, q.beta = T, q.sig = T, q.z = T, quiet = T)

Arguments

filedir character. The name of the output directory created by BGmix.
q.beta logical. Read beta values?
q.sig logical. Read gene variance parameters?
q.z logical. Read z values?
quiet logical. Parameter passed to 'scan'. (If false, 'scan' prints details of number of items read in.)

Value

mbeta matrix no. genes x no. effects. Posterior means of gene effect parameters (usually gene means and log fold changes).
msig2 matrix no. genes x no. variances. Posterior means of gene variances.
mbb vector of hyperparameters (b) for gene variances (posterior means).
maa vector of hyperparameters (a) for gene variances (posterior means).
mtau matrix no. genes x no. conditions. Posterior means of gene precisions.
mwtc vector of posterior mean mixture weights
mzg vector of posterior mean allocation for each gene
meta vector of mixture parameters (eta)
mlambda vector of mixture parameters (lambda)
pc matrix no. genes x no. mixture components. Posterior probability for each gene of being classified into each mixture component.

Author(s)

Alex Lewin

Examples

## Note this is a very short MCMC run!
## For good analysis need proper burn-in period.
data(ybar,ss)
outdir <- BGmix(ybar, ss, c(8,8), nburn=0, niter=100, nthin=1)
params <- ccParams(outdir)

[Package BGmix version 1.2.0 Index]