designMatrix           package:ArrayTools           R Documentation

_C_l_a_s_s _t_o _C_o_n_t_a_i_n _t_h_e _D_e_s_i_g_n _M_a_t_r_i_x _t_h_a_t _U_s_e_d _f_o_r _L_i_n_e_a_r _R_e_g_r_e_s_s_i_o_n

_D_e_s_c_r_i_p_t_i_o_n:

     Class to Contain the Design Matrix that Used for Linear Regression

_C_r_e_a_t_i_n_g _O_b_j_e_c_t_s:

     'new("designMatrix", ..., target, covariates, intIndex=0)'

     This create as design matrix class.  'target' is a data frame that
     contains chip and covaraite information, or experimental
     phenotypes  recorded in eSet and ExpressionSet-derived classes. 
     'covariates' is a list of 1-n covariates.  If 'intIndex=0', the
     interaction effect  is not considered; otherwise, use two integers
     to indicate which  covariates are considered for interaction
     effect. For example,  if 'covariates <-
     c("estrogen","drug","time")' and you are considering  the
     interaction between "estrogen" and "time", then you would write 
     'intIndex=c(1,3)'

_S_l_o_t_s:


     '_d_e_s_i_g_n': contains the design matrix

     '_t_a_r_g_e_t': contains the 'target' data

     '_c_o_v_a_r_i_a_t_e_s': contains the 'covariates'

     '_i_n_t_I_n_d_e_x': contains the 'intIndex'

_M_e_t_h_o_d_s:


     _g_e_t_C_o_v_a_r_i_a_t_e_s 'signature(object = "designMatrix")':  access the
          'covariates' slot 

     _g_e_t_D_e_s_i_g_n 'signature(object = "designMatrix")':   access the
          'design' slot

     _g_e_t_I_n_t_I_n_d_e_x 'signature(object = "designMatrix")':   access the
          'intIndex' slot

     _g_e_t_T_a_r_g_e_t 'signature(object = "designMatrix")':   access the
          'target' slot

     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "designMatrix")':   create a new
          designMatrix class

     _s_h_o_w 'signature(object = "designMatrix")':   print the
          designMatrix class

_A_u_t_h_o_r(_s):

     Xiwei Wu, Arthur Li

_S_e_e _A_l_s_o:

     'contrastMatrix'

_E_x_a_m_p_l_e_s:

     data(eSetExample)
     ## One-way Anova
     (design1<- new("designMatrix", target=pData(eSetExample), covariates = "Treatment"))

     ## Randomized block design
     (design2<- new("designMatrix", target=pData(eSetExample), 
        covariates = c("Treatment", "Group")))

     ## Interaction design
     (design3<- new("designMatrix", target=pData(eSetExample), 
        covariates = c("Treatment", "Group"), intIndex=c(1,2)))
        

