conditionLevel           package:designGG           R Documentation

_L_e_v_e_l_s _o_f _a_l_l _e_n_v_i_r_o_n_m_e_n_t_a_l _f_a_c_t_o_r_s

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

     Describe the levels of all environmental factors for each
     RIL/strain in the experiment.
      This is a subfunction needed for 'designScore', but is not
     directly used.

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

         conditionLevel( array.allocation, condition.allocation, 
                         condition.combination,nEnvFactors )

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

array.allocation: a matrix with nArray rows and nRIL columns. Elements
          of 1/0 indicates this RIL (or strain) is/not selected  for
          this array. 

condition.allocation: a matrix with nCondition rows and nRIL columns.
          Elements of 1/0 indicates this RIL (or strain) is/not
          selected  for this condition. 

condition.combination: a matrix indicating all possible levels for
          environmental factors,  with dimension of nConditions by
          nEnvFactors. 

nEnvFactors: number of environmental factors, an integer bewteen 1 and
          3. When 'nEnvFactors' is 1 and 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. 

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

     For single-channel experiment, 'array.allocation' is 'NULL'. Then
     the 'conditionLevel' is  decided by 'condition.allocation'. For
     dual-channel experiment, 'array.allocation' decides which RILs are
     selected and then the 'condition.allocation' indicates which
     condition this RIL will be put in for the experiment.

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

     A matrix with dimension of nRILs by nEnvFactors, each element
     indicates the  level of a certain environmental factor to which
     the RIL (or strain) is exposed in the  experiment.

_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', 'conditionCombination'

