readGenes.pfizer        package:GeneticsBase        R Documentation

_R_e_a_d _g_e_n_e_t_i_c_s _d_a_t_a _f_i_l_e_s _t_h_a_t _u_s_e _P_f_i_z_e_r'_s _d_a_t_a _f_o_r_m_a_t.

_D_e_s_c_r_i_p_t_i_o_n:

     Read genetics data files that use Pfizer's data format.

_U_s_a_g_e:

     readGenes.pfizer(filename, phase=list(F),
                      format=c("Pivot", "Listing"),...)

_A_r_g_u_m_e_n_t_s:

filename: Name of the file in which data is stored 

   phase: see below

  format: Format of the file to be read, one of "Pivot" or "Listing"

     ...: Additional arguments to function read.table

_D_e_t_a_i_l_s:

     The argument 'phase' may be:

   _1 A single logical scalar value that applies for all markers

   _2 A logical vector with one element per marker

   _3 A phaseObject (TBD) providing observation by marker by phase
        probabilities + definitions of contigs + probability of contigs


_V_a_l_u_e:

     a geneSet object

_A_u_t_h_o_r(_s):

     Gregory R. Warnes warnes@bst.rochester.edu and Nitin Jain
     nitin.jain@pfizer.com

_E_x_a_m_p_l_e_s:

     # store where we are now
     here <- getwd()

     # move to the data directory
     dir <- file.path(.path.package("GeneticsBase"),"data")
     setwd(dir)

     # load Pfizer Data
     PfizerExample <- readGenes.pfizer("PfizerExample.txt", format="Listing")

     # look at the data
     PfizerExample

     # return to the original path
     setwd(here)

