variableNames            package:designGG            R Documentation

_G_e_n_e_r_a_t_e _v_a_r_i_a_b_l_e _n_a_m_e_s _f_o_r _a_l_l _f_a_c_t_o_r_s

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

     Generate variable names for genetic, environmental factors and
     interacting terms.

_U_s_a_g_e:

     variableNames(nEnvFactors)

_A_r_g_u_m_e_n_t_s:

nEnvFactors: number of environmental factors, an integer bewteen 1 and
          3. When 'nEnvFactors' is 1 and the number of levels for the
          enviromental factor  ('nLevels')is 1, there is one condition
          in the experiment (i.e. no  enviromental perturbation) and
          thus only genetic factor will be considered in the algorithm.
          When 'nEnvFactors' is 1 and nLevels is larger than 1 or
          'nEnvFactors' is larger than 1, all main factor(s) and
          interacting facotr(s) will be included. Examples: If there is
          a temperature perturbation, then 'nEnvFactors' is 1; If there
          is both temperature and drug treatment perturbation,  then
          'nEnvFactors' is 2. 

_D_e_t_a_i_l_s:

     generates names for variables, a vector with the length of 
     (variableNumber+1).

_V_a_l_u_e:

     When 'nEnvFactors' = 1 and 'nLevels' = 1, there is no environmetal
     pertubation in the experimental. Then we re-define 'nEnvFactors'
     to be 0 within the algorithm. Accordingly, 'variableNumber' = 1,
     and 'variableNames' is one genetic factor "Q".  
      When 'nEnvFactors' = 1, 'variableNumber' = 3, and 'variableNames'
     are one genetic factor "Q", one environmental factor "F", and one
     interacting factor "QxF". 
         When 'nEnvFactors' = 2, 'variableNumber' = 7, and
     'variableNames' are one genetic factor "Q", two environmental
     factors "F1" and "F2",  three two-way interacting factors "QF1",
     "QF2", "F1F2",  and one three way interacting factors "QxF1xF2".  
      When 'nEnvFactors' = 3,  'variableNumber' = 15, and
     'variableNames' are one genetic factor "Q", three environmental
     factors "F1", "F2" and "F3", six two-way interacting factors
     "QF1", "QF2", "QF3", "F1F2", "F2F3" and "F1F3", four three-way
     interacting factors "QxF1xF2", "QxF1xF3", "QxF2xF3", "F1xF2xF3" 
     and one four-way interacting factors "QxF1xF2xF3".

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

     Yang Li <yang.li@rug.nl>, Gonzalo Vera
     <gonzalo.vera.rodriguez@gmail.com> 
      Rainer Breitling <r.breitling@rug.nl>, Ritsert Jansen
     <r.c.jansen@rug.nl>

_R_e_f_e_r_e_n_c_e_s:

     Y. Li, R. Breitling and R.C. Jansen. Generalizing genetical
     genomics: the added value from environmental perturbation, Trends
     Genet (2008) 24:518-524. 
      Y. Li, M. Swertz, G. Vera, J. Fu, R. Breitling, and R.C. Jansen.
     designGG: An R-package and Web tool for the optimal design of
     genetical genomics experiments. (submitted) 
      http://gbic.biol.rug.nl/designGG

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

     'variableNumber '

