init.Para.CNA: Initial parameters for the HMM

In genoCN: genotyping and copy number study tools

Description

a list of initial values for the parameters of genoCNA.

Usage

data(init.Para.CNA)

Format

The format is a list of 16 items

• 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, indicating the upper/lower bound of mu.r

• sd.r.upper, sd.r.lower two vectors of the same size of sd.r, indicating 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 maximum 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, indicating the upper/lower bound of sd.b

• trans.m transition probability matrix of size N*N. The diagonal 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 chromosome, therefore it is a matrix of 1*N.

Examples

data(init.Para.CNA)

genoCN documentation built on Nov. 8, 2020, 8:12 p.m.