addsamptree: To determine whether the sampled tree will be accepted

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

Description

To determine whether the sampled tree will be accepted by comparing the likelihood, used in canopy.sample.

Usage

addsamptree(tree,tree.new)

Arguments

tree	input tree (current)
tree.new	input tree (newly sampled)

Value

returned tree (either retain the old tree or accept the new tree).

Author(s)

Yuchao Jiang [e-mail]

Examples

data(MDA231)
data(MDA231_tree)
sna.name = MDA231$sna.name
Y = MDA231$Y
C = MDA231$C
R = MDA231$R
X = MDA231$X
WM = MDA231$WM
Wm = MDA231$Wm
epsilonM = MDA231$epsilonM
epsilonm = MDA231$epsilonm
# sampling location of SNAs
tree.new = MDA231_tree
tree.new$sna = sampsna(MDA231_tree)
tree.new$Z = getZ(tree.new, sna.name)
tree.new$Q = getQ(tree.new, Y, C)
tree.new$H = tree.new$Q
tree.new$VAF = getVAF(tree.new, Y)
tree.new$likelihood = getlikelihood(tree.new, R, X, WM, Wm, epsilonM, epsilonm)
tree = addsamptree(MDA231_tree,tree.new)

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