init.Para.CNA {genoCN}R Documentation

Initial parameters for the HMM

Description

a list of initial values for the parameters of the HMM, either for copy number abberation (CNA) studies or for copy number variation (CNV) studies.

Usage

data(init.Para.CNA)
data(init.Para.CNV)

Format

The format is: List of 16

pi.r
a vector of length N, where N is the number of states. pi.r[j] is the prior probability of the uniform component of log R ratio for state j
mu.r
a vector of length N, where N is the number of states. mu.r[j] is mean value of the normal component of log R ratio for state j
sd.r
a vector of length N, where N is the number of states. sd.r[j] is standard deviation of the normal component of log R ratio for state j
mu.r.upper, mu.r.lower
two vectors of the same size of mu.r, incating the upper/lower bound of mu.r
sd.r.upper, sd.r.lower
two vectors of the same size of sd.r, incating the upper/lower bound of sd.r
pi.b
a vector of length N, where N is the number of states. pi.b[j] is the prior probability of the uniform component of B allele frequency for state j
mu.b
a matrix of N*M, where N is the number of states, and M is the miximum number of components of each states. mu.b[i,j] indicates the mean value of the j-th component of the i-th state
sd.b
a matrix of the same size of mu.b, specifying the standard deviations
mu.b.upper, mu.b.lower
two matrices of the same size of mu.b, incating the upper/lower bound of mu.b
sd.b.upper, sd.b.lower
two matrices of the same size of sd.b, incating the upper/lower bound of sd.b
trans.m
transition probability matrix of size N*N. The diagnal elements are not used.
trans.begin
a matrix of size S*N, where S is the number of chromosomes, and N is the number of states. trans.begin[s,] are the state probabilities for the fist probe of the s-th chromosome. By default, we assume there is only one chromsome, therefore it is a matrix of 1*N.

Examples

data(init.Para.CNA)

[Package genoCN version 1.04 Index]