conditionAllocation         package:designGG         R Documentation

_A_l_l_o_c_a_t_e _t_h_e _s_e_l_e_c_t_e_d _R_I_L_s _i_n_t_o _d_i_f_f_e_r_e_n_t _c_o_n_d_i_t_i_o_n_s

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

     This is a subfunction used by 'initialDesign' but is not directly
     used. In  the experiment where samples are profiled in pairs, the
     samples are firstly selected and paired on each array and then the
     selected samples are randomly allocated into different conditions.

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

       conditionAllocation( selectedRILs, genotype, nConditions, nSlides, nTuple )

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

selectedRILs: the index of the selected RILs or strains among all that
          are available for the experiment.  

genotype: genotype data: a nMarker-by-nRILs matrix with two allels
          being 0 and 1 (or A and B) or three allels being 0, 0.5 and 1
          (or, A, H, and B), where 0.5 (or H) represents heterozygous
          allele. 

nConditions: number of all possible combination of all environmental
          factors. It should be larger than 1.  

 nSlides: total number of slides available for the experiment. It
          should be a non-zero integer. 

  nTuple: average number of RILs to be assigned onto each condition. 
           'nTuple' should be a real number which is larger than 1.
           if 'nTuple' < 1, the algorithm will stop and show a message
          as below, 
           'warning: "The number of slides is too small to perform the
          experiment."' 

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

     This function is only called by 'initialDesign' function when
     'btwoColorArray' is 'TRUE'.

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

     A matrix with nCondition rows and nRIL columns. Elements of 1/0
     indicate that this RIL (or strain) is/not selected for this
     condition.

_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:

     'initialDesign'

