canopy.post {Canopy} | R Documentation |
Burnin, thinning, and posterior evaluation of MCMC sampled trees.
canopy.post(sampchain, projectname, K, numchain, burnin, thin, optK, C, post.config.cutoff)
sampchain |
list of sampled trees returned by |
projectname |
name of project |
K |
number of subclones (vector) |
numchain |
number of MCMC chains with random initiations |
burnin |
burnin of MCMC chains |
thin |
MCMC chain thinning. |
optK |
optimal number of subclones determined by |
C |
CNA and CNA-region overlapping matrix, only needed if overlapping CNAs are used as input |
post.config.cutoff |
cutoff value for posterior probabilities of tree configurations, default is set to be 0.05 (only tree configurations with greater than 0.05 posterior probabilities will be reported by Canopy) |
samptreethin |
list of sampled posterior trees |
samptreethin.lik |
vector of likelihood of sampled posterior trees |
config |
vector of configuration of sampled posterior trees (integer values) |
config.summary |
summary of configurations of sampled posterior trees |
Yuchao Jiang yuchaoj@wharton.upenn.edu
data(MDA231_sampchain) data(MDA231) sampchain = MDA231_sampchain projectname = 'MD231' K = 3:6 numchain = 20 burnin = 150 thin = 5 optK = 4 C = MDA231$C post = canopy.post(sampchain = sampchain, projectname = projectname, K = K, numchain = numchain, burnin = burnin, thin = thin, optK = optK, C = C)