HVDMcheck               package:rHVDM               R Documentation

_C_h_e_c_k_s _t_h_a_t _a_n _o_b_j_e_c_t _o_f _c_l_a_s_s _E_x_p_r_e_s_s_i_o_n_S_e_t _i_s _c_o_m_p_l_i_a_n_t _w_i_t_h _H_V_D_M

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

     This method issues warnings about the compliance of the
     ExpressionSet object to be used with rHVDM. It just issues
     warnings and does not attempt to correct the problems encountered.
     the 'pdata' argument is optional; if missing, the method will
     check the phenodata that is inside the ExpressionSet.

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

     HVDMcheck(eset,pdata)

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

    eset: an ExpressionSet object (Biobase) 

   pdata: a dataframe (optional argument) 

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

     The checks performed are: A) the phenoData has all the required
     fields. B) the time field is numeric, has a zero time point, does
     not have negative or repeated values. C) the row names in the
     phenoData  are consistent with the columns names found in the
     ExpressionSet. D) the data are not log-transformed. E) Standard
     deviations have been supplied in the ExpressionSet, and they are
     non-negative.

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

     no value returned.

_N_o_t_e:

     If the 'pdata' argument is ignored (it can be),  the method checks
     the phenoData that is inside the ExpressionSet.

_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'

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

     data(HVDMexample)
     HVDMcheck(fiveGyMAS5)

