makeped                 package:gap                 R Documentation

_A _f_u_n_c_t_i_o_n _t_o _p_r_e_p_a_r_e _p_e_d_i_g_r_e_e_s _i_n _p_o_s_t-_M_A_K_E_P_E_D _f_o_r_m_a_t

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

     Many computer programs for genetic data analysis requires pedigree
     data to be in the so-called  ``post-MAKEPED'' format. This
     function performs this translation and allows for some 
     inconsistences to be detected.

     The first four columns of the input file contains the following
     information:

     pedigree ID, individual ID, father's ID, mother's ID, sex

     Either father's or mother's id is set to 0 for founders, i.e.
     individuals with no parents.  Numeric coding for sex is 0=unknown,
     1=male, 2=female. These can be followed by satellite  information
     such as disease phenotype and marker information.

     The output file has extra information extracted from data above.

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

     makeped(pifile="pedfile.pre", pofile="pedfile.ped", auto.select=1,
            with.loop=0, loop.file=NA, auto.proband=1, proband.file=NA)

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

  pifile: input filename

  pofile: output filename

auto.select: no loops in pedigrees and probands are selected
          automatically? 0=no, 1=yes

with.loop: input data with loops? 0=no, 1=yes

loop.file: filename containing pedigree id and an individual id for
          each loop, set if with.loop=1

auto.proband: probands are selected automatically? 0=no, 1=yes

proband.file: filename containing pedigree id and proband id, set if
          auto.proband=0 (not implemented)

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

     Before invoking makeped, input file, loop file and proband file
     have to be prepared.

     By default, auto.select=1, so translation proceeds without
     considering loops and proband statuses. If there are loops in the
     pedigrees, then set auto.select=0, with.loop=1,
     loop.file="filespec".

     There may be several versions of makeped available, but their
     differences with this port should  be minor.

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

     All output will be written in pofile

_N_o_t_e:

     adapted from makeped.c by W Li and others

_S_o_u_r_c_e:

     <URL: http://linkage.rockefeller.edu>

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

     ## Not run: 
     library(gap)
     makeped("ped7.pre","ped7.ped",0,1,"ped7.lop")
     ## End(Not run)

