read.series.FCS           package:rflowcyt           R Documentation

_R_e_a_d_i_n_g _a _s_e_r_i_e _o_f _r_a_w _b_i_n_a_r_y _F_l_o_w _C_y_t_o_m_e_t_r_y _S_t_a_n_d_a_r_d (_F_C_S) _f_i_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Reads a serie of raw Flow Cytometry Standard (FCS) files and
     outputs several "FCS" R object.

_U_s_a_g_e:

     read.series.FCS(fcsfiles,path=NULL,ext=NULL,...)

_A_r_g_u_m_e_n_t_s:

fcsfiles: names of the FCS files without any extension

    path: a character vector of full path names; the default
          corresponds to the working directory 'getwd'

     ext: character string giving optional extension to be added to
          each file name

     ...: any other arguments are passed to 'read.FCS'

_D_e_t_a_i_l_s:

     This function read several FCS files by the means of the
     'read.FCS' function. Thus,this function can also checks if there
     are discrepancies between the data and the metadata in terms of
     range and size (MY.DEBUG=TRUE).  If there is, then the data is
     re-read with different fcs.byte.size (1,2,4,8) and fcs.signed
     (TRUE, FALSE) combinations until there is no discrepancy between
     the data and the metadata.  If there is still a discrepancy, then
     the routine is halted.  Note: For FCS version 3.0 files, only the
     range of the data is checked against what is stated in the
     metadata because FCS version 3.0 files have extra elements that
     are read into the data.

_V_a_l_u_e:

     No value is returned. However a series of "FCS" object are created
     on the current environment with names of the form filename. The
     files names are given by the elements of slides. Each object is
     composed of the same data and metadata return by the 'read.FCS'
     function.

_A_u_t_h_o_r(_s):

     N. Le Meur

_S_e_e _A_l_s_o:

     'read.FCS', 'summary', 'print', 'extractGatedData',
     'addParameter', '"[-methods"', '"[[-methods"', 'fcs.type'
     'readCytoSet'

_E_x_a_m_p_l_e_s:

      if (require(rfcdmin)) {

      ##obtaining the location of the fcs files in the data
       pathFiles<-system.file("bccrc", package="rfcdmin")
       drugFiles<-dir(pathFiles)

      ## reading in the FCS files
       drugData<-read.series.FCS(drugFiles,path=pathFiles,MY.DEBUG=FALSE)
       }

