HVDMreport               package:rHVDM               R Documentation

_g_e_n_e_r_a_t_e_s _a_n _H_T_M_L _r_e_p_o_r_t _u_s_i_n_g _t_h_e _i_n_p_u_t

_D_e_s_c_r_i_p_t_i_o_n:

     This method generates report using one of the HVDM outputs (either
     from the 'training()', 'screeening()' or 'fitgene()' commands.)

_U_s_a_g_e:

     HVDMreport(HVDM,name)

_A_r_g_u_m_e_n_t_s:

    HVDM: a list output either by a 'training()', 'screening()' or
          'fitgene()' command.

    name: an optional argument allowing to specify the name of the HTML
          file (the .HTML extension is added automatically). 

_D_e_t_a_i_l_s:

     If the output has been generated by 'training()' or 'fitgene()',
     the HTML report contains four sections:

     1) Functions inputs.

     2) Model score.

     3) Fitted parameters.

     4) Visual comparison of model and data.

     In the 'fitgene()' case comparisons with correponding results for
     genes in the training set are given.

     If the output has been generated by the 'screening()' command, the
     HTML report contains the following sections:

     1) Inputs to the preceding 'training()' command.

     2) Inputs to the 'screening()' command (such as bounds used to
     classify genes).

     3) Results.

     4) List of putative targets of the transcription factor under
     review.

     The HTML report is genereated in the current working directory.
     Graphic files are stored in a subdirectory with a similar name.

_V_a_l_u_e:

     Nothing is returned, but a message indicating the name of the HTML
     file and its location on the hard drive is given.

_N_o_t_e:

     The HTML report is generated in the working directory.

_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','fitgene'

_E_x_a_m_p_l_e_s:

     data(HVDMexample)
     tHVDMp53<-training(eset=fiveGyMAS5,genes=p53traingenes,degrate=0.8,actname="p53")
     #HVDMreport(tHVDMp53)
     #HVDMreport(tHVDMp53, name="p53training")

