pedAFreq                package:fbat                R Documentation

_g_e_t _a_l_l_e_l_e _f_r_e_q_u_e_n_c_i_e_s

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

     Get allele frequencies (missing alleles allowed).

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

     pedAFreq(geneSetObj, founderOnly=TRUE, quiet=FALSE)

     pedAFreq.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 pid (pedigree
          id), id (individual id), fid (father id), mid (mother id),
          sex, aff (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","affect") 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:

aFreqMat: allele frequencies.

aPercMat: allele 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<-pedAFreq(CAMP)
       res$aFreqMat
       res$aPercMat

