"checkvars-methods"         package:rflowcyt         R Documentation

_C_h_e_c_k_s _t_h_e _r_a_n_g_e_s, _d_i_m_e_n_s_i_o_n_s, _a_n_d _n_a_m_e_s _o_f _t_h_e _m_e_t_a_d_a_t_a _b_a_s_e_d _o_n _t_h_e
_c_u_r_r_e_n_t _d_a_t_a _o_f _a_n _F_C_S _R-_o_b_j_e_c_t.

_D_e_s_c_r_i_p_t_i_o_n:

     Any discrepancy between the metadata and the data of the FCS
     object is considered as a failure to pass the check.  The
     following is a description of the checks:

_1. _D_i_m_e_n_s_i_o_n _c_h_e_c_k We always check the dimensions (ie, if the data
     dimensions match with size ("$TOT") and nparam ("$PAR") that are
     specified in the metadata).   

_2. _P_a_r_a_m_e_t_e_r _N_a_m_e _c_h_e_c_k We check the names of the metadata with the
     names of the data column parameters.  Either only the longnames
     ("$PnS") or the shortnames ("$PnN") of the metadata are checked
     against the names of the data.  Please take note that both
     ("$PnS") and ("$PnN") ARE NOT BOTH checked. 

_3. _C_o_l_u_m_n _V_a_r_i_a_b_l_e _R_a_n_g_e _C_h_e_c_k We check the paramranges ("$PnR")
     specified in the metadata with the column parameter ranges of the
     data; if the paramranges do not exist in the metadata, then it is
     noted in the debugging statements.

     Please note that if the metadata@original is FALSE, then the
     metadata slotNames have a  "RFACSadd$>>$" suffix and are located
     in metadata@fcsinfo in order to store the current data
     descriptives. The original data descriptives can be
     retrieved/checked when metadata@original is set to TRUE; otherwise
     the current metadata information about the data is
     retrieved/checked even when the "RFACSadd$>>$" suffix is not noted
     in the character index.

     (ie) If metadata@original is FALSE, then metadata[["size"]] will
     return metadata[["RFACSadd$>>$$TOT"]], the current row length of
     the data, while metadata@size will return the number of rows for
     the original data.

     Note that metadata@original is changed only when a parameter
     column is added to the data using 'addParameter-methods', when
     rows of the data are extracted using 'extractGatedData' or if the
     user decides to change the value metadata@original.  Using
     '"["-methods' and '"[<-"-methods' on a "FCS" object will not
     change the value of metadata@original.

_M_e_t_h_o_d_s:


     _x = "_F_C_S" boolean value is returned; TRUE if the check passes and
          FALSE if it does not pass the check.

     _x = "_F_C_S", _M_Y._D_E_B_U_G=_T_R_U_E, _r_a_n_g_e._m_a_x=_N_U_L_L Other options in the
          signature include:

          (1) MY.DEBUG : boolean value; if TRUE, then the output
          statements are printed, otherwise if FALSE, then the
          statements are surpressed; default is TRUE.

          (2) range.max : numeric value describing the true maximum of
          the data that the checks on the ranges will be compared;
          default is NULL (ie, the maximum of each column variable in
          the data is the truth)

