doProbeLinear         package:GeneRegionScan         R Documentation

_D_o _P_r_o_b_e _L_i_n_e_a_r

_D_e_s_c_r_i_p_t_i_o_n:

     Internal function used to calculate linear correlation between
     probe level intensity and factorial pData entries such as
     genotypes.

_U_s_a_g_e:

         doProbeLinear(object, label, testType="linear model")

_A_r_g_u_m_e_n_t_s:

  object: A ProbeLevelSet object or a regular ExpressionSet object.

   label: An optional character string specifying a column name in the
          pData of the object. If this argument is given, the gene plot
          will be colour coded based on the different groups (factors)
          in the pData entry. If a summaryType other than 'dots' is
          selected the summarisation is done stratified by the
          different groups in the pData.

testType: Character string, defining a statistic procedure to identify
          especially interesting probes.

_D_e_t_a_i_l_s:

     This function is not meant to be called by the user. It does the
     statistical calculations when called by plotStatistics.

     One important note about the assumption that the alphabetical
     order is the same as value order. This usually works with SNP
     datatypes of the type AA, AB, BB. However the sorting is locale
     dependent and can produce odd results, which is why the value
     assignments are always printed. See Comparison for details on
     this. Further user-control over this aspect of  the plotting
     function was omitted, giving more weight to the simplicity of the
     function interface. In case of problems it  is recommended to
     rename the entries in the label so that they will be correctly
     sorted.

_V_a_l_u_e:

     A correlation list with p-value and fold-change in columns and
     probe IDs as rownames. Used by plotStatistics when decorating
     plots from plotOnGene.

_A_u_t_h_o_r(_s):

     Lasse Folkersen

_S_e_e _A_l_s_o:

     'plotStatistics', 'plotOnGene'

_E_x_a_m_p_l_e_s:

             data(exampleProbeLevelSet)
             colnames(pData(exampleProbeLevelSet))
             linearModelData<-GeneRegionScan:::doProbeLinear(exampleProbeLevelSet,"genotype3")
             colnames(linearModelData)
             #P value for the probe with ID 679083 in relation to "genotype3"
             print(linearModelData["679083","p-value"])

