missGFreq                package:fbat                R Documentation

_C_o_u_n_t _f_r_e_q_u_e_n_c_i_e_s _o_f _m_i_s_s_i_n_g _g_e_n_o_t_y_p_e_s

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

     Count frequencies of missing genotypes

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

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

     missGFreq.default(pedObj, founderOnly=TRUE)

_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

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

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

     A matrix with the following three columns: 

column 1: counts of genotypes, of which both alleles are missing.

column 2: counts of genotypes, of which the first allele is missing and
          the second allele is not missing.

column 3: counts of genotypes, of which the first allele is not missing
          and the second allele is missing.

_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<-missGFreq(CAMP,founderOnly=FALSE)
       # number of missing genotypes per marker
       print(res$nMissMarkers)
       # number of missing genotypes per subject
       print(res$nMissSubjects[1:10,])

