pedGFreq                package:fbat                R Documentation

_g_e_t _g_e_n_o_t_y_p_e _f_r_e_q_u_e_n_c_i_e_s

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

     Get genotype frequencies (missing alleles allowed).

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

     pedGFreq(geneSetObj, founderOnly=TRUE, missingOutput=FALSE, quiet=FALSE)

     pedGFreq.default(pedObj, 
              founderOnly=TRUE,
              missingOutput=FALSE,
              quiet=FALSE)

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

geneSetObj: a 'geneSet' object.

  pedObj: a list with five elements: 'ped', 'columns', 'markerNames',
          'Position', and 'filename'. 'ped' is a pedigree data frame
          whose first 6 columns are family (pedigree id), pid (patient
          id), father (father id), mother (mother id), sex, affected
          (affection status). The remaining columns are pairs of marker
          alleles. Each row corresponds to an individual; 'columns' are
          the names of the first 5 (or 6) columns of ped file. It
          should be either equal to 
          c("family","pid","father","mother","sex","affected") or equal
          to c("family","pid","father","mother","sex"); 'founderOnly'
          indicates if using only founder info; 'markerNames' is a
          vector of marker names; 'Position' is a vector of marker
          positions; 'fileName' is the pedigree file name

founderOnly: indicates if using only founder info.

missingOutput: indicates if missing allele frequency should be output.

   quiet: print intermediate results if 'quiet=FALSE'.

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

gFreqMat: genotype frequencies.

gPercMat: genotype percentages.

missingOutput: indicates if missing allele frequency should be output.

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

     Weiliang Qiu stwxq@channing.harvard.edu,  Ross Lazarus
     ross.lazarus@channing.harvard.edu,  Gregory Warnes
     warnes@bst.rochester.edu, Nitin Jain nitin.jain@pfizer.com

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

       data(CAMP)
       res<-pedGFreq(CAMP)
       res$gFreqMat
       res$gPercMat

