alias.glmNA             package:Envisage             R Documentation

_F_i_n_d _A_l_i_a_s_e_s (_D_e_p_e_n_d_e_n_c_i_e_s) _i_n _a _M_o_d_e_l

_D_e_s_c_r_i_p_t_i_o_n:

     Find aliases (linearly dependent terms) in a linear model
     specified by a formula. This extends the S3 method 'alias' to
     objects of class 'glmNA' for package 'Envisage'.

_U_s_a_g_e:

       ## S3 method for class 'glmNA':
       alias(object, ...) 

_A_r_g_u_m_e_n_t_s:

  object: A fitted model object of class 'glmNA'.

     ...: Further arguments passed to or from other methods.

_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 'alias.glmNA' extends the method 'alias' to the S4
     class 'glmNA' for package 'Envisage'. This is an extension of
     classes 'glm' and 'lm' and deals appropriately with genes that
     produce NA calls in the modelling procedure. This allows use of
     the function 'Anova' for calculating significance for each gene. 

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

_V_a_l_u_e:

     A list (of class "listof") containing components:

   Model: Description of the model; usually the formula.

Complete: A matrix with columns corresponding to effects that are
          linearly dependent on the rows.

 Partial: The correlations of the estimable effects, with a zero
          diagonal. An object of class "mtable" which has its own print
          method.

_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:

     'coef', 'glmNA. For the main \pkg{Envisage} method, see
     \code{envisage}.'

