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]