init.Para.CNV: Initial parameters for the HMM of genoCNV
Description
a list of initial values for the parameters genoCNV.
Usage
data(init.Para.CNV)
Arguments
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,
incating 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.