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, quiet=FALSE)

     pedGFreq.default(ped, 
              columns=c("family","pid","father","mother","sex","affected"),
              founderOnly=TRUE,
              quiet=FALSE)

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

geneSetObj: a 'geneSet' object.

     ped: 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: 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

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

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

gFreqMat: genotype frequencies.

gPercMat: genotype percentages.

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

     Weiliang Qiu stwxq@channing.harvard.edu, Ross Lazarus
     ross.lazarus@channing.harvard.edu

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

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

