Classify                package:RLMM                R Documentation

_C_l_a_s_s_i_f_i_c_a_t_i_o_n _o_f _S_N_P_s _b_a_s_e_d _o_n _t_h_e_t_a _e_s_t_i_m_a_t_e_s

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

     This function entails classification of SNPs based on the theta
     estimates (thetafile), genotype information (A regions file), and
     some internal files. Currently, this algorithm works for the
     Affymetrix 100K - Xba dataset.

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

     Classify(genotypefile = "",
              regionsfile = "",
              thetafile = "",
              callrate = 100)
             

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

genotypefile: Name of the classified SNPs with the genotypes (required)

regionsfile: Character string specifying the directory AND name of
          regionsfile - e.g., "Xba.regions" (required)

thetafile: Character string specifying the directory AND name of
          thetafile (required)

callrate: Call Rate percentage; The user can specify any number from
          the list: 80,82,84,86,88,90,92,94,96,98,100. Default is
          100%(optional)

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

     For each SNP, Mahalanobis distances from each chip's (theta A,
     theta B) ordered pair to the genotype centers is calculated. Each
     chip is assigned the genotype of the cluster which it is closest
     to (ie: AA, AB, BB).

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

     Nusrat Rabbee <nrabbee@post.harvard.edu>, Gary Wong
     <wongg62@gmail.com>

