summaryGeno           package:haplo.stats           R Documentation

_S_u_m_m_a_r_i_z_e _F_u_l_l _H_a_p_l_o_t_y_p_e _E_n_u_m_e_r_a_t_i_o_n _o_n _G_e_n_o_t_y_p_e _M_a_t_r_i_x

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

     Provide a summary of missing allele information for each
     individual  in the genotype matrix.  The number of loci missing
     zero, one, or two  alleles is computed, as well as the total
     number of haplotype pairs  that could result from the observed
     phenotype.

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

     summaryGeno(geno, miss.val=0)

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

    geno: Matrix of alleles, such that each locus has a pair of
          adjacent columns of alleles, and the order of columns
          corresponds to the order of loci  on a chromosome. If there
          are K loci, then geno has 2*K columns. Rows  represent all
          observed alleles for each subject. 

miss.val : Vector of codes for allele missing values. 

_D_e_t_a_i_l_s:

     After getting information on the individual loci, this function
     makes  a call to geno.count.pairs().  The E-M steps to estimate
     haplotype  frequencies considers haplotypes that could result from
     a phenotype with a missing allele.  It will not remove a subject's
     phenotype, only the unlikely haplotypes that result from it.

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

     Data frame with columns representing the number of loci with zero,
     one, and two missing alleles, then the total haplotype pairs
     resulting from full enumeration of the phenotype.

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

     'geno.count.pairs', 'haplo.em'

