XdeParameter-class            package:XDE            R Documentation

_C_o_n_t_a_i_n_e_r _c_l_a_s_s _f_o_r _s_t_o_r_i_n_g _o_p_t_i_o_n_s _o_f _t_h_e _B_a_y_e_s_i_a_n _h_i_e_r_a_r_c_h_i_c_a_l _m_o_d_e_l

_D_e_s_c_r_i_p_t_i_o_n:

     This class contains initial values for the first iteration of the
     MCMC, options for saving MCMC chains, options for changing the
     tuning parameters of the Metropolis-Hastings algorithm, options
     for changing hyperparameters from their defaults, etc.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("XdeParameter",
     esetList, updates, tuning, hyperparameters, output, iterations,
     burnin, seed, randomSeed, genes, studies, firstMcmc,
     specifiedInitialValues, directory, phenotypeLabel, showIterations,
     verbose, studyNames)'.

_S_l_o_t_s:


     '_u_p_d_a_t_e_s': Object of class 'numeric'. The frequency of  updates
          for each iteration of the chain.

     '_t_u_n_i_n_g': Object of class 'numeric'.  Tuning parameters for the
          Metropolis-Hastings proposals 

     '_h_y_p_e_r_p_a_r_a_m_e_t_e_r_s': Object of class 'numeric'. Hyperparameters for
          the Bayesian hierarchical model

     '_o_u_t_p_u_t': Object of class 'numeric'. Indicator for whether to save
          the MCMC chain to file.  If the value is zero, the chain is
          not saved.

     '_i_t_e_r_a_t_i_o_n_s': Object of class 'numeric'.  The total number of MCMC
          iterations.

     '_b_u_r_n_i_n': Object of class 'logical'.  If set to FALSE, by default
          none of the chains will be saved (called for its side-effect
          of setting the output to zero for each parameter).

     '_n_o_t_e_s': Object of class 'character'. 

     '_f_i_r_s_t_M_c_m_c': Object of class 'environment'. Values for the first
          iteration of the MCMC 

     '_s_h_o_w_I_t_e_r_a_t_i_o_n_s': Object of class 'logical'. Whether to show the
          MCMC iteration when fitting the model

     '_s_p_e_c_i_f_i_e_d_I_n_i_t_i_a_l_V_a_l_u_e_s': Object of class 'logical'.  If TRUE (the
          default), the values stored in 'firstMcmc' will be used for
          the first iteration of the MCMC. 

     '_d_i_r_e_c_t_o_r_y': Object of class 'character'. Specifies where to write
          the log files

     '_p_h_e_n_o_t_y_p_e_L_a_b_e_l': Object of class 'character'. The name of the
          binary covariate used for differential expression 

     '_v_e_r_b_o_s_e': Object of class 'logical' 

     '_s_t_u_d_y_N_a_m_e_s': Object of class 'character'. Names of the datasets

_M_e_t_h_o_d_s:


     _b_u_r_n_i_n 'signature(object = "XdeParameter")' logical. See 'burnin'

     _b_u_r_n_i_n<- 'signature(object = "XdeParameter", value = "logical")'
          logical. See 'burnin'

     _d_i_r_e_c_t_o_r_y 'signature(object = "XdeParameter")' character string
          giving the path or relative path to store log files from the
          MCMC chain

     _d_i_r_e_c_t_o_r_y<- 'signature(object = "XdeParameter")'Path to store log
          files. 

     _f_i_r_s_t_M_c_m_c 'signature(object = "XdeParameter")' See 'firstMcmc'

     _f_i_r_s_t_M_c_m_c<- 'signature(object = "XdeParameter", value =
          "environment")' 

     _f_i_r_s_t_M_c_m_c<- 'signature(object = "XdeParameter", value = "list")' 

     _h_y_p_e_r_p_a_r_a_m_e_t_e_r_s 'signature(object = "XdeParameter")' See the
          XdeParameterClass vignette

     _h_y_p_e_r_p_a_r_a_m_e_t_e_r_s<- 'signature(object = "XdeParameter")' See the
          XdeParameterClass vignette

     _i_n_i_t_i_a_l_i_z_e 'signature(.Object = "XdeParameter")' Method for
          initializing an instance of the class.  The default values
          provided work well in most cases.

     _i_t_e_r_a_t_i_o_n_s 'signature(object = "XdeParameter")' Accessor for the
          total number of MCMC iterations to run

     _i_t_e_r_a_t_i_o_n_s<- 'signature(object = "XdeParameter", value = numeric)'
          The replacement method is useful for setting a different
          number of iterations.

     _i_t_e_r_a_t_i_o_n_s<- 'signature(object = "XdeParameter", value =
          "integer")' 

     _o_u_t_p_u_t 'signature(object = "XdeParameter")' See also 'output'.
          This method is also defined for class 'XdeMcmc'

     _o_u_t_p_u_t<- 'signature(object = "XdeParameter")' See also 'output' 

     _p_h_e_n_o_t_y_p_e_L_a_b_e_l 'signature(object = "XdeParameter")' The name of a
          binary covariate present in each study

     _p_h_e_n_o_t_y_p_e_L_a_b_e_l<- 'signature(object = "XdeParameter", value =
          "character")' 

     _s_a_v_e_d_I_t_e_r_a_t_i_o_n_s 'signature(object = "XdeParameter")' The number of
          MCMC iterations written to file.  It is the value of the
          total number of iterations divided by the thinning parameter.
           See also 'output'

     _s_e_e_d 'signature(object = "XdeParameter")' See 'seed'

     _s_e_e_d<- 'signature(object = "XdeParameter", value="integer")'
          Replacement method. See also 'seed'.    

     _s_h_o_w 'signature(object = "XdeParameter")' Produces a short summary
          of objects that are instances of the 'XdeParameter' class

     _s_h_o_w_I_t_e_r_a_t_i_o_n_s 'signature(object = "XdeParameter")' logical

     _s_h_o_w_I_t_e_r_a_t_i_o_n_s<- 'signature(object = "XdeParameter")' 

     _s_t_u_d_y_N_a_m_e_s 'signature(object = "XdeParameter")' Names of the
          high-throughput gene expression studies

     _s_t_u_d_y_N_a_m_e_s<- 'signature(object = "XdeParameter")' 

     _t_h_i_n 'signature(x = "XdeParameter")' See 'output' and 'thin'

     _t_h_i_n<- 'signature(x = "XdeParameter", value = numeric)' See 'thin'

     _t_u_n_i_n_g 'signature(object = "XdeParameter")' See also 'tuning'

     _t_u_n_i_n_g<- 'signature(object = "XdeParameter")' 

     _u_p_d_a_t_e_s 'signature(object = "XdeParameter")' See also 'updates'

     _u_p_d_a_t_e_s<- 'signature(object = "XdeParameter")' 

_A_u_t_h_o_r(_s):

     R. Scharpf

_R_e_f_e_r_e_n_c_e_s:

     R. Scharpf

_S_e_e _A_l_s_o:

     'ExpressionSetList-class'

_E_x_a_m_p_l_e_s:

     showClass("XdeParameter")
     ##See the XdeParameterClass vignette

