addSnpPdata          package:GeneRegionScan          R Documentation

_A_d_d _S_N_P _d_a_t_a _f_r_o_m _h_a_p_m_a_p-_s_t_y_l_e _d_a_t_a _f_i_l_e _t_o _p_D_a_t_a _o_f _E_x_p_r_e_s_s_i_o_n_S_e_t

_D_e_s_c_r_i_p_t_i_o_n:

     Function that will add genotypes to an ExpressionSet when given a
     data file with genotypes in the same format as outputted by
     http://www.hapmap.org.

_U_s_a_g_e:

         addSnpPdata(object, listOfSnps)

_A_r_g_u_m_e_n_t_s:

  object: A ProbeLevelSet object or a regular ExpressionSet object (in
          which case a probeData argument is required). See
          getLocalProbeIntensities and related functions on how to
          create a ProbeLevelSet.

listOfSnps: A character string giving the path of a file containing SNP
          data in the same format as used by the export function of
          www.hapmap.org.

_D_e_t_a_i_l_s:

     A function that takes an ExpressionSet and the path for a
     SNP-file. The SNP-file should have the same format as  files
     downloaded from http://www.hapmap.org. The function then checks if
     the sampleNames are present in the SNP-file. If they are, it
     decorates the ExpressionSet with the SNPs. If the snp name already
     exists as a column name in the pData, the function tries to merge
     the new information from listOfSnps with the new. Original NA
     values are overwritten by new values. Original values that are the
     same as new values are kept the same. Original values that are not
     the same as new values are preserved in their original state and a
     warning is given.

_V_a_l_u_e:

     The same ProbeLevelSet or ExpressionSet given as argument, but
     with the SNP type data added to the pData and with the extra
     information of the listOfSnps file added to the notes section.

_A_u_t_h_o_r(_s):

     Lasse Folkersen

_S_e_e _A_l_s_o:

     'getLocalProbeIntensities','plotOnGene'

_E_x_a_m_p_l_e_s:

             ## Not run: 
             hapmapformatdata<-"~/somefile.txt"
             probelevelsetwithsnps<-addSnpPdata(probelevelset,hapmapformatdata)
             
     ## End(Not run)

