getlikelihood {Canopy}

To get likelihood of the tree

Description

To get likelihood of the tree given tree struture and data input. Used in canopy.sample.

Usage

getlikelihood(tree,R,X,WM,Wm,epsilonM,epsilonm)

Arguments

tree

input tree

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)

Value

Likelihood of sampled tree.

Author(s)

Yuchao Jiang [e-mail]

Examples

data(MDA231)
data(MDA231_tree)
R = MDA231$R
X = MDA231$X
WM = MDA231$WM
Wm = MDA231$Wm
epsilonM = MDA231$epsilonM
epsilonm = MDA231$epsilonm
getlikelihood(MDA231_tree, R, X, WM, Wm, epsilonM, epsilonm)