ccTrace {BGmix} | R Documentation |
Read trace files from BGmix
Description
Reads output files containing whole posterior distributions from BGmix. Also calls 'ccSummary', and outputs model options.
Usage
ccTrace(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 variances? |
q.z |
logical. Read z values? |
quiet |
logical. Parameter passed to 'scan'. (If false,
'scan' prints details of number of items read in.) |
Value
summ |
list object output by 'ccSummary' |
eta |
matrix (no. components -1) x no. MCMC samples. Posterior of mixture component parameters (eta). |
lambda |
matrix (no. components -1) x no. MCMC samples. Posterior of mixture component parameters (lambda). |
aa |
matrix no. MCMC samples x no. variances. Posterior of variance hyperparameters (a). |
bb |
matrix no. MCMC samples x no. variances. Posterior of variance hyperparameters (b). |
wtc |
matrix no. MCMC samples x no. mixture components. Posterior of mixture weights. |
beta |
matrix no. effects x no. genes x no. MCMC samples. Posterior of gene effects. |
sig2 |
matrix no. variances x no. genes x no. MCMC samples. Posterior of gene variances. |
zg |
matrix no. MCMC samples x no. genes. Posterior of gene allocations. |
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)
tr <- ccTrace(outdir)
[Package
BGmix version 1.2.0
Index]