pedFlagHomo               package:fbat               R Documentation

_f_l_a_g _h_o_m_o/_h_e_t_e_r_o_z_y_g_o_t_e_s

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

     Flag homo/heterozygotes.

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

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

     pedFlagHomo.default(pedObj, 
                 founderOnly=TRUE,
                 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

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

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

countMat: Count the number of homo/heterozygotes.

flagHomoMat: Flag homo/heterozygotes. 1 - homozygotes; 0 -
          heterozygotes; -1 - genotype contains one missing allele; -2
          - genotype contains two missing alleles.

markerNames: marker names.

_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<-pedFlagHomo(CAMP)
       res$countMat
       res$flagHomoMat
       res$markerNames

