fitgene                package:rHVDM                R Documentation

_F_i_t_s _t_h_e _o_p_t_i_m_a_l _k_i_n_e_t_i_c _p_a_r_a_m_e_t_e_r _v_a_l_u_e_s _f_o_r _a _p_a_r_t_i_c_u_l_a_r _g_e_n_e.

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

     This method fits the three kinetic parameter values for a
     particular gene. It returns a list containing the results.

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

     fitgene(eset,gene,tHVDM,transforms,firstguess)

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

    eset: an ExpressionSet object (Biobase) 

    gene: the gene identifier in character format 

transforms: a vector containing the kinetic parameter identifiers that
          have to be transformed during optimisation (optional) 

   tHVDM: the output of the training set 

firstguess: first guess for the fitting (optional, see details)

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

     An exponential transform is set by default for both the basal (Bj)
     and degradation (Dj) rates (through the transforms argument). This
     forces the values for both these parameters to be positive. It
     also helps to reach a better fit. To turn this off let
     'transforms=c()'. Even in this case the degradation rate will not
     be allowed to take non positive values as it causes problems with
     the differential operator used internally. The value in the vector
     indicates the parameter to be transformed: "Bj": basal rate of
     transcription, "Sj": sensitivity, "Dj": degrdation rate. The entry
     label indicates the transform to be applied; presently, only
     log-transforms are implemented (ie "exp").

     This 'fitgene()' step can only be applied after a 'training()'
     step. The output to the 'training()' step has to be fed through 
     the 'tHVDM' argument.

     The 'firstguess' argument is optional (a first guess is generated
     internally by default).  However a first guess can be supplied by
     the user which can take several forms.  It can either be a vector
     with three entries containing a first guess for the basal rate, 
     the sensitivity, the degradation rate (in that order). 
     Alternatively, another output from the 'fitgene()' function (for
     example from a gene that has a similar expression profile) can be
     supplied as a 'firstguess' argument.

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

     a list containing the results (see documentation for more
     details).

_N_o_t_e:

     Obviously, the expression set given as a 'eset' argument has to be
     the same as the one used for the training step.

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

     Martino Barenco

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

     M. Barenco, D. Tomescu, D. Brewer, R. Callard, J. Stark, M. Hubank
     (2006) Ranked predictions of p53 targets using Hidden Variable
     Dynamic Modelling. _Genome Biology_, *V7(3)*, R25.

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

     'training','screening','HVDMreport'

_E_x_a_m_p_l_e_s:

     data(HVDMexample)
     tHVDMp53<-training(eset=fiveGyMAS5,genes=p53traingenes,degrate=0.8,actname="p53")
     sHVDMcd38<-fitgene(eset=fiveGyMAS5,gene="205692_s_at",tHVDM=tHVDMp53)

