interactionLevel          package:designGG          R Documentation

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

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

     Generate levels for all interacting factors for all RILs (or
     strains). This is a subfunction needed for 'designScore', but is
     not directly used.

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

       interactionLevel( genotype.level, condition.level, markerIndex, 
                         nEnvFactors )

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

genotype.level: levels of genetic factor for each RIL (or strain) in
          the experiment.   

condition.level: levels of all environmental factors for each RIL (or
          strain)in the experiment.  

markerIndex: indicate which genome position that level of genetic
          factor corresponds to.  

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:

     'markerIndex' indicates the genome position that 'genotype.level'
     corresponds to.
       An experiment design is defined to be optimal over all markers
     if  the sum of scores, e.g. A-optimality criterion over all
     markers is  minimized.

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

     a matrix with nRILs rows. The number columns depends on
     'nEnvFactors'. For example: 
      If 'nEnvFactors' = 1, there is only one interaction term. 
      If 'nEnvFactors' = 2, there are three pair-wise two-way
     interaction terms and one  three-way interaction term.

_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:

     'designScore', 'conditionLevel'

