readLink                package:fbat                R Documentation

_I_m_p_o_r_t _f_i_l_e _w_i_t_h _P_L_I_N_K _d_a_t_a _f_o_r_m_a_t

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

     Import file with PLINK data format and convert it to a pedigree
     object.

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

     readLink(pedfile, gmfile, columns = c("family", "pid", "father", "mother", "sex"), quiet = FALSE)

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

 pedfile: pedigree data file with no marker info

  gmfile: marker info files. It contains three columns: marker IDs,
          marker names, and marker positions

 columns: By default, the first five columns of 'pedfile' are sample
          information: family id, patient id,  father id, mother id,
          patient sex.

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

_D_e_t_a_i_l_s:

     The data format is used by the software PLINK.

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

     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.

_N_o_t_e:

_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

_R_e_f_e_r_e_n_c_e_s:

_S_e_e _A_l_s_o:

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

