"fixvars-methods"          package:rflowcyt          R Documentation

_C_h_e_c_k_s _a_n_d _f_i_x_e_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 and will be
     updated with the descriptives from the data. The following is a
     description of the checks and fixes:

_1. _D_i_m_e_n_s_i_o_n _c_h_e_c_k _a_n_d _f_i_x We always check the dimensions (ie, if the
     data dimensions match with size ($TOT) and nparam ($PAR) that are
     specified in the metadata.  If they are not in check, then the
     metadata parameters are changed to reflect the values of the data
     dimensions.    

_2. _P_a_r_a_m_e_t_e_r _N_a_m_e _c_h_e_c_k _a_n_d _f_i_x 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.  Depending on the number
     of discrepancies (ie, the one with the least number of
     discrepanices; by default the longnames if there is a tie), either
     the longnames or the shortnames  of the metadata are replaced with
     the column names of the data. 

_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 there are any discrepancies, then the paramranges are
     replaced with the maximum values of the data columns.

     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" A 'FCS'object will be returned with any fixes to the
          metadata.

     _x = "_F_C_S", _x._n_a_m_e="", _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) x.name : character string of the true object name;
          default is "" (ie, the objectname in the metadata will be
          regarded as the true object name )

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

          (3) 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)


