readHapMap               package:fbat               R Documentation

_I_m_p_o_r_t _H_a_p_M_a_p _d_a_t_a

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

     Import HapMap data and convert it to pedigree format.

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

     readHapMap(hapmapfile, race="CEU", skip = 2, comment.char = "&", quiet = FALSE)

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

hapmapfile: the hapmap file name

    race: can take values 'CEU', 'YRI', 'CHB', and 'JPT'

    skip: first 'skip' lines in the file 'hapmapfile' will be skipped.

comment.char: hapmapfile snp names contain the symbol # which is the
          comment command of R. So by default, we set 'comment.char' as
          &.

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

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

     HapMap files are those snp files output by HapMap browsers.

_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:

