ccParams

0th

Percentile

Read posterior means and classification probabilities from BGmix

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

Keywords
manip
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.

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

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