transitionProbability       package:VanillaICE       R Documentation

_C_o_m_p_u_t_e _t_h_e _t_r_a_n_s_i_t_i_o_n _p_r_o_b_a_b_i_l_i_t_y

_D_e_s_c_r_i_p_t_i_o_n:

     Wrapper for computing the locus-specific transition probability

_U_s_a_g_e:

     transitionProbability(chromosome, position, TAUP = 1e+08, chromosomeAnnotation, verbose = FALSE)

_A_r_g_u_m_e_n_t_s:

chromosome: chromosome (integer representation)

position: physical position

    TAUP: Scalar for computing transition probabilities (see Details).

chromosomeAnnotation: Optional: chromosome annotation

 verbose: Logical: verbose output

_D_e_t_a_i_l_s:

     The HMM uses locus-specific transition probabilities that are
     calculated as a function of the physical distance between loci.
     Specifically, the probability that the locus at position t-1 is
     not informative for the locus at position t is calculated as
     1-exp(-d/TAUP), where d is the physical distance between locus t
     and locus t-1.  The default for TAUP is 1 x 10^8 and can be
     specified to acheive a desired amount of sensitivity and
     specificity.  Larger values of TAUP decreases the probability of
     transitioning to other states, and therefore provides a more
     smooth fit.

_V_a_l_u_e:

     The transitionProbability function (i) transforms the physical
     distance between adjacent loci to an estimate of the genomic
     distance and (ii) adds an 'arm' variable to the annotation matrix.

chromosome: chromosome 

position: physical position

     arm: an integer.  The HMM uses the arm variable as a factor and is
          fit independently to each 'arm'.

transitionPr: locus-specific transition probabilities

_A_u_t_h_o_r(_s):

     R. Scharpf

_S_e_e _A_l_s_o:

     'chromosomeAnnotation'

