conditionCombination        package:designGG        R Documentation

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_f_a_c_t_o_r_s

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

     Generate a matrix indicating all possible levels for environmental
      factors with dimension nConditions $\times$ nEnvFactors. This is
     a subfunction needed for 'designScore', but is not directly used.

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

       conditionCombination( nEnvFactors, nLevels, Level, envFactorNames )

_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. 

 nLevels: number of levels for each factor, a vector with each 
          component being integer. The length should be equal to 
          'nEnvFactors'. 

   Level: a list which specifies the levels for each factor in the
          experiment. There are in total 'nEnvFactors' elements in the
          list and each element correspsonds to certain envrironmental
          factor. The element is a vector describing all levels of the
          environmental factor. Default setting for the level of each
          factor is 1, 2, ...., nLevels[i]. (Here nLevels[i] is the
          _i_th element of nLevels, which tells the total number of
          levels for _i_ environmental factor). 

envFactorNames: a vector with names for all environmental factor(s).
          For example, for an experiment with two environmental factors
          of temperature and drug treatment: 'envFactorNames <- c(
          "Temperature", "Dosage" ) '
           Default = 'NULL', then the output will use '"F1"' and '"F2"'
          to indicate the environmental factors. 

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

     Currently this function works only when 'nEnvFactors' is between 1
     and 3.

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

     A matrix with dimension of nConditions $\times$ nEnvFactors. Each
     element in the matrix indicates the levels of corresponding
     environmental factor.

_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'

