convertS3toS4            package:rflowcyt            R Documentation

_C_o_n_v_e_r_t_s _S_3 _c_l_a_s_s _F_C_S _o_b_j_e_c_t _t_o _S_4 _c_l_a_s_s _F_C_S _o_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     This function will update any S3 class 'FCS' object to S4 class.

_U_s_a_g_e:

     convertS3toS4(S3file, myFCSobj.name = "", fileName = "")

_A_r_g_u_m_e_n_t_s:

  S3file: S3 Class FCS object location and filename

myFCSobj.name: character string indicating the FCS object name 

fileName: character string indicating the file name of the binary raw
          FCS data, from which the FCS object originates and which is
          read by 'read.FCS'

_D_e_t_a_i_l_s:

     The FCS object is obtained as the result of 'read.FCS' which has
     been currently updated to output FCS objects as class S4 instead
     of S3.

_V_a_l_u_e:

     A Class S4 'FCS' object with the following slots: 

    data: matrix of the data, where the rows are the cells/observations
          and the columns are the different fluoroescence measurements

metadata: of class 'FCSmetadata' with the following slots:

     _m_o_d_e the mode of the raw binary file

     _s_i_z_e numeric value describing the total number of rows or
          observations/cells

     _n_p_a_r_a_m numeric value describing the number of columns or
          parameters

     _s_h_o_r_t_n_a_m_e_s a vector of the short names of the column variables of
          the data

     _l_o_n_g_n_a_m_e_s a vector of the long names of the column variables of
          the data

     _p_a_r_a_m_r_a_n_g_e_s the vector of corresponding ranges or maximum values
          for each column variable

     _f_i_l_e_n_a_m_e character string of the name of the raw data file from
          which the object originates

     _o_b_j_e_c_t_n_a_m_e character string of the name of the FCS S4 object

     _o_r_i_g_i_n_a_l Boolean value indicating whether the data is the original

     _f_c_s_i_n_f_o list of other parameters 

_A_u_t_h_o_r(_s):

     A.J. Rossini and J.Y. Wan

_S_e_e _A_l_s_o:

     'read.FCS', 'FCS'

_E_x_a_m_p_l_e_s:

       if (require(rfcdmin)){

          ## if previously read-in as S3 FCS object
          facscan256.fcs<- paste(system.file("fcs", package="rfcdmin"),
                                   "facscan256.fcs",
                                   sep="/")

          ## reading in the FCS files
          FCSobj.S3<-read.FCS(facscan256.fcs, UseS3=TRUE)

          ## convert to S4 FCS

          FCSobj.S4<- convertS3toS4(FCSobj.S3,
                                    myFCSobj.name="FCSobj.S4",
                                    fileName=facscan256.fcs)
       }

