coef.glmNA             package:Envisage             R Documentation

_E_x_t_r_a_c_t _M_o_d_e_l _C_o_e_f_f_i_c_i_e_n_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     'coef' is a generic function which extracts model coefficients
     from objects returned by modeling functions. 'coefficients' is an
     _alias_ for it. This extends the S3 method  'coef' to objects of
     class 'glmNA' for package 'Envisage'.

_U_s_a_g_e:

       ## S3 method for class 'glmNA':
       coef(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 'coef.glmNA' extends the method 'coef' to the S4
     class 'glmNA' for package 'Envisage'. This is an extension of
     classes 'glm' and 'lm' and deals appropriately with the model
     output for 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:

     Coefficients extracted from the model object 'object'.

_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:

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

