readFCS                package:prada                R Documentation

_R_e_a_d _a_n _F_C_S _f_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     Read one or several FCS files: Data File Standard for Flow
     Cytometry

_U_s_a_g_e:

       read.fcs(filename=NULL, objectModel="prada", ...)
       readFCS(filename)

_A_r_g_u_m_e_n_t_s:

filename: Character of length 1: filename

objectModel: Character of length 1: the object model to use for the
          output. Either 'prada' for 'cytoFrame' objects or 'FCS' for
          'rflowcyt''s 'FCS' objects.

     ...: Arguments that get passed on to higher-level import
          functions.

_D_e_t_a_i_l_s:

     The function 'readFCS' works with the output of the FACS machine
     software from a number of vendors. However, the FCS 3.0 standard
     includes some options that are not yet implemented in this
     function. If you need extensions, please let me know. The output
     of the fucntion is an object of class 'cytoFrame'.

     'read.fcs' is a wrapper function that allows the user to specify
     the class of the output. The purpose of the function is to
     standardize the way flow cytometry data is imported into R using
     the 'prada' or 'rflowcyt' packages. If the 'filename' argument to
     'read.fcs' is a character vector of 'length > 1', multiple FCS
     files can be imported. Please see the documentation for
     'readCytoSet' and 'read.series.FCS' for alternatives ways to
     import multiple FCS files and for more details on the higher-level
     import function.

     Be aware that 'rflowcyt' needs to be installed when the function
     is run with argument 'objectModel="FCS"'.

     For specifications of FCS 3.0 see <URL: http://www.isac-net.org>
     and the file <URL: ../doc/fcs3.html> in the 'doc' directory of the
     package.

_V_a_l_u_e:

     An object of class 'cytoFrame' or 'FCS'.

_A_u_t_h_o_r(_s):

     Wolfgang Huber <URL: http://www.ebi.ac.uk/huber>, Florian Hahne

_S_e_e _A_l_s_o:

     'read.FCS', 'read.series.FCS', 'readCytoSet'

_E_x_a_m_p_l_e_s:

     sampdat <- readFCS(system.file("extdata", "fas-Bcl2-plate323-04-04.A01",
                                    package="prada"))
     files <- dir(system.file("extdata", package="prada"),
                  pattern="[A-H][0-9][0-9]")
     sampdat2 <- read.fcs(system.file("extdata", "fas-Bcl2-plate323-04-04.A01",
                                    package="prada"))
     sampdat3 <- read.fcs(files, path=system.file("extdata", package="prada"))
     sampdat
     exprs(sampdat[1:3,])
     description(sampdat)[3:6]
     class(sampdat3)

