canopy.sample: MCMC sampling in tree space

In Canopy: Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing

Description

To sample the posterior trees. Major function of Canopy.

Usage

canopy.sample(R, X, WM, Wm, epsilonM, epsilonm, C=NULL,
              Y, K, numchain, max.simrun, min.simrun, writeskip, projectname,
              cell.line=NULL, plot.likelihood=NULL)

Arguments

R	alternative allele read depth matrix
X	total read depth matrix
WM	observed major copy number matrix
Wm	observed minor copy number matrix
epsilonM	observed standard deviation of major copy number (scalar input is transformed into matrix)
epsilonm	observed standard deviation of minor copy number (scalar input is transformed into matrix)
C	CNA and CNA-region overlapping matrix, only needed if overlapping CNAs are used as input
Y	SNA and CNA-region overlapping matrix
K	number of subclones (vector)
numchain	number of MCMC chains with random initiations
max.simrun	maximum number of simutation iterations for each chain
min.simrun	minimum number of simutation iterations for each chain
writeskip	interval to store sampled trees
projectname	name of project
cell.line	default to be FALSE, TRUE if input sample is cell line (no normal cell contamination)
plot.likelihood	default to be TRUE, posterior likelihood plot generated for check of convergence and selection of burnin and thinning in canopy.post

Value

List of sampleed trees in subtree space with different number of subclones; plot of posterior likelihoods in each subtree space generated (pdf format).

Author(s)

Yuchao Jiang [e-mail]

Examples

data(MDA231)
R = MDA231$R; X = MDA231$X
WM = MDA231$WM; Wm = MDA231$Wm
epsilonM = MDA231$epsilonM; epsilonm = MDA231$epsilonm
C = MDA231$C
Y = MDA231$Y
K = 3:6
numchain = 20
projectname = 'MDA231'
# sampchain = canopy.sample(R = R, X = X, WM = WM, Wm = Wm, epsilonM = epsilonM, 
#             epsilonm = epsilonm, C = C, Y = Y, K = K, numchain = numchain, 
#             max.simrun = 50000, min.simrun = 10000, writeskip = 200, 
#             projectname = projectname, cell.line = TRUE, plot.likelihood = TRUE)

Canopy documentation built on May 1, 2019, 7:59 p.m.