haplo               package:haplo.ccs               R Documentation

_S_p_e_c_i_f_y _a_n _A_l_l_e_l_e _M_a_t_r_i_x, _I_n_h_e_r_i_t_a_n_c_e _M_o_d_e, _a_n_d _G_r_o_u_p_i_n_g _f_o_r _R_a_r_e _H_a_p_l_o_t_y_p_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     'haplo' specifies an allele matrix and an inheritance mode for the
     'haplo.ccs' model formula. 'haplo' also specifies preferences for
     grouping rare haplotypes.

_U_s_a_g_e:

     haplo(..., mode, group.rare=TRUE, rare.freq=0.02)

_A_r_g_u_m_e_n_t_s:

     ...: a matrix of alleles or list of columns of an allele matrix.
          Each locus on the chromosome has a pair of adjacent columns
          in the allele matrix, so that the number of columns of the
          allele matrix is twice the number of loci on the chromosome.
          The order of the columns corresponds to the order of the loci
          on the chromosome, and each row corresponds to the alleles
          for each subject.  The alleles should be numerically coded,
          i.e., 1, 2, 3, or 4 for 'A', 'C', 'G', or 'T'.

    mode: the inheritance mode, either 'additive', 'dominant', or
          'recessive'. Note that the default inheritance mode is
          'additive'.

group.rare: a logical value indicating whether rare haplotypes should
          be grouped in the 'haplo.ccs' model. Note that the default is
          to group rare haplotypes.

rare.freq: the population haplotype frequency to define rare
          haplotypes. If 'group.rare=TRUE', then haplotypes with an
          estimated population frequency less than or equal to
          'rare.freq' are grouped in the 'haplo.ccs' model. Note that
          the default haplotype frequency is 0.02. 'rare.freq' is
          automatically set to 0 if 'group.rare=FALSE'.

_V_a_l_u_e:

     A matrix of alleles with mode, group.rare, and rare.freq assigned
     as attributes.

_A_u_t_h_o_r(_s):

     Benjamin French and Thomas Lumley, University of Washington

_R_e_f_e_r_e_n_c_e_s:

     French B, Lumley T, Monks SA, Rice KM, Hindorff LA, Reiner AP,
     Psaty BM. Simple estimates of haplotype relative risks in
     case-control data. Genetic Epidemiology 2006; 30(6):485-494.

_S_e_e _A_l_s_o:

     'haplo.ccs'

_E_x_a_m_p_l_e_s:

     data(renin)

     ## Specify an allele matrix in a model fit by 'haplo.ccs'.

     haplo.ccs(case ~ haplo(geno))

     ## Specify dominant inheritance and define rare haplotypes.

     haplo.ccs(case ~ haplo(geno, mode="dominant", rare.freq=0.01))

     ## Specify the allele matrix without grouping rare haplotypes.

     haplo.ccs(case ~ haplo(geno, group.rare=FALSE))

