ccTrace

0th

Percentile

Read trace files from BGmix

Reads output files containing whole posterior distributions from BGmix. Also calls 'ccSummary', and outputs model options.

Keywords
manip
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.

Aliases
  • ccTrace
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)
Documentation reproduced from package BGmix, version 1.32.0, License: GPL-2

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