modelEntry             package:Envisage             R Documentation

_S_p_e_c_i_f_y _a _m_i_n_i_m_u_m _m_o_d_e_l _f_o_r _s_t_e_p-_w_i_s_e _m_o_d_e_l _f_i_t_t_i_n_g

_D_e_s_c_r_i_p_t_i_o_n:

     This function allows specification of a minimum model for the
     step-wise model fitting procedure in the 'Envisage' GUI. This can
     'force' terms of interest to always be considered in the model for
     each gene.

_U_s_a_g_e:

       modelEntry(pData, Mentry, useParams, labParams, MEorINT, glm.formula) 

_A_r_g_u_m_e_n_t_s:

   pData: An object of class 'phenoData' containing the phenotypic
          information for the experiment.

  Mentry: Object of class 'tkentry' containing the model entry field
          from the 'Envisage' GUI. This is used if the starting model
          is specified in the GUI.

useParams: Character vector containing the variable names to be used in
          the model fitting procedure.

labParams: Output from function 'labelParams', containing the indices
          of the labelling parameters for the 'phenoData' object
          'pData'.

 MEorINT: Character string indicating whether to look at main effect
          terms only (''ME'') or main effect and interaction terms
          (''INT'').

glm.formula: Object of class 'formula' containing the minimal model for
          the step-wise model fitting procedure.

_D_e_t_a_i_l_s:

     The 'Envisage' package contains methods allowing the use of 
     linear models (LMs) for analysing significantly changing genes in 
     experiments with a variety of sources of variation, be they
     experimentally controlled variables such as drug treatment or
     time, or non-controlled sources of confounding variation such as
     phenotypic or environmental differences. This allows all sources
     of variation to be considered when analysing for significant
     differential expression, ensuring resulting genes are biologically
     relevent to the experimental question. 

     The function 'modelEntry' is used to set up the maximum and
     minimum models for the 'Envisage' step-wise model fitting
     procedure. This can be done in one of two ways. If using the
     command line interface to 'envisage', the model can be explicitly
     stated in the command line in the form  'X ~ var1 + var2:var3 +
     etc.'. However, if using the GUI ('widget=TRUE'), users can
     specify the model in terms of the variable labels (of the form
     'p1', 'p2', 'p3', etc. (e.g. 'p1+p3+p5:p6'). This function
     processes these values to give the minimum model for the analysis.

     'modelEntry' is an internal function and is not designed to be
     accessed by users.

_V_a_l_u_e:

     A list is returned with the followig slots:

startingModel: An object of class 'formula' giving the minimum model
          for the the step-wise model fitting procedure.

  intPos: An internal object used to identify the location of
          interaction terms within the minimum model.

_A_u_t_h_o_r(_s):

     Sam Robson S.C.Robson@warwick.ac.uk

_R_e_f_e_r_e_n_c_e_s:

     Robson, S. C., Hunter, E., Bird, H., Turner, H. (2008)  _Envisage:
     model-based significance analysis of microarray gene expression
     data_, manuscript in preparation

_S_e_e _A_l_s_o:

     For the main 'Envisage' method, see 'envisage'.

