SNP2Geno               package:SimHap               R Documentation

_C_o_n_v_e_r_t _b_i_a_l_l_e_l_i_c _S_N_P _d_a_t_a _t_o _g_e_n_o_t_y_p_e _c_o_u_n_t _d_a_t_a

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

     Converts biallelic SNP data to the format required by SNP analysis
     functions

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

     SNP2Geno(geno, baseline)

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

    geno: A data frame containing biallelic SNP data. The first column
          should contain a subject identifier. The remaining columns
          should each represent a biallelic SNP, containing two alleles
          per entry with no separator.

baseline: A vector of character strings representing the 'wildtype'
          genotype.

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

     'SNP2Geno' uses 'baseline' to recode biallelic SNP data into a
     series of columns representing genotype counts under additive,
     dominant and recessive models. The genotype specified as the
     wildtype will always be recoded as 0. Under an additive model, the
     heterozygote is recoded as 1 and the minor homozygote is recoded
     as 2. Under a dominant model, both the heterozygote and minor
     homozygote are recoded as 1, and under a recessive model, the
     heterozygote is recoded as 0 and the minor homozygote is coded as
     1.

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

     'SNP2Geno' returns a data frame whose first column is a subject
     identifier. The remaining columns comprise 3 per SNP where the
     first is recoded under an additive model, the second is recoded
     under a dominant model and the third is recoded under a recessive
     model.

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

     Pamela A. McCaskie

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

     'SNP2Haplo'

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

     data(SNP.dat)
     geno.dat <- SNP2Geno(SNP.dat, baseline=c("MM", "11", "GG", "CC"))

