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 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,
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 1.06
Index]