fcs.type              package:rflowcyt              R Documentation

_O_b_j_e_c_t_s _p_r_o_v_i_d_i_n_g _p_a_r_a_m_e_t_e_r_s _f_o_r _t_h_e _r_a_w _F_C_S _f_i_l_e _t_y_p_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     The 'fcs.type' objects define the parameters needed for reading in
     certain raw FCS files into R via the use of 'read.FCS'. Currently
     this is just a script file defining certain 'fcs.type' objects,
     but ultimately this will be an environment.  There are certain
     'read.FCS' parameters that are known to be compatible for certain
     types of cytometers.  The 'fcs.type' objects may be optionally
     used during the reading in of raw FCS files into R and result in
     FCS R-objects (FCS objects).

_U_s_a_g_e:

        fcs.type.default

_A_r_g_u_m_e_n_t_s:

     No arguments.

_D_e_t_a_i_l_s:

     A fcs.type is a list of the following:

_v_e_r_s_i_o_n raw FCS version number; value$=$"1.0" or "2.0" or "3.0"

_b_y_t_e._s_i_z_e The byte size for the file (8 bits is one byte); value=1 or 2
     or 4, etc.

_s_i_g_n_e_d boolean; If the data is signed; value$=$FALSE or TRUE

_e_n_d_i_a_n The endian of the file depending on the endian of the platform;
     Usually the value of endian is "big" (if both the file and
     platform endian are "big") or "little" (if both the platform and
     the file endian are "little") or  "auto", then the read.FCS will
     automatically detect the endian compatibility with the platform
     system (See 'readBin' for more details.) 

     The fcs.types are the following:

_1.  _f_c_s._t_y_p_e._d_e_f_a_u_l_t a list of the following options and values: 

_v_e_r_s_i_o_n "2.0"

_b_y_t_e._s_i_z_e 2

_s_i_g_n_e_d TRUE

_e_n_d_i_a_n "auto"

_2.  _f_c_s._t_y_p_e._c_e_l_l_q_u_e_s_t._3._1._F_A_C_S_c_a_n a list of the following options and
     values:

_v_e_r_s_i_o_n "2.0"

_b_y_t_e._s_i_z_e 1

_s_i_g_n_e_d FALSE

_e_n_d_i_a_n "auto"

_3.  _f_c_s._t_y_p_e._L_S_R_2_5_6 a list of the following options and values:

_v_e_r_s_i_o_n "2.0"

_b_y_t_e._s_i_z_e 1

_s_i_g_n_e_d FALSE

_e_n_d_i_a_n "auto"

_4.  _f_c_s._t_y_p_e._F_A_C_S_t_a_r_2_5_6 a list of the following options and values:

_v_e_r_s_i_o_n "2.0"

_b_y_t_e._s_i_z_e 1

_s_i_g_n_e_d FALSE

_e_n_d_i_a_n "auto"

_5.  _f_c_s._t_y_p_e._f_a_c_s_c_a_n_2_5_6 a list of the following options and values:

_v_e_r_s_i_o_n "2.0"

_b_y_t_e._s_i_z_e 1

_s_i_g_n_e_d FALSE

_e_n_d_i_a_n "auto"

_6.  _f_c_s._t_y_p_e._c_e_l_l_q_u_e_s_t._3._1._F_A_C_S._V_a_n_t_a_g_e a list of the following options
     and values: 

_v_e_r_s_i_o_n "2.0"

_b_y_t_e._s_i_z_e 2

_s_i_g_n_e_d TRUE

_e_n_d_i_a_n "auto"

_7.  _f_c_s._t_y_p_e._c_e_l_l_q_u_e_s_t._3._3 a list of the following options and values: 

_v_e_r_s_i_o_n "2.0"

_b_y_t_e._s_i_z_e 2

_s_i_g_n_e_d TRUE

_e_n_d_i_a_n "auto"

_8.  _f_c_s._t_y_p_e._L_Y_S_Y_S a list of the following options and values: 

_v_e_r_s_i_o_n "2.0"

_b_y_t_e._s_i_z_e 2

_s_i_g_n_e_d TRUE

_e_n_d_i_a_n "auto"

_9.  _f_c_s._t_y_p_e._D_i_V_a_1_0_2_4 a list of the following options and values: 

_v_e_r_s_i_o_n "2.0"

_b_y_t_e._s_i_z_e 2

_s_i_g_n_e_d TRUE

_e_n_d_i_a_n "auto"

_1_0. _f_c_s._t_y_p_e._F_A_C_S_C_a_l_i_b_u_r_1_0_2_4 a list of the following options and
     values: 

_v_e_r_s_i_o_n "2.0"

_b_y_t_e._s_i_z_e 2

_s_i_g_n_e_d TRUE

_e_n_d_i_a_n "auto"

_1_1. _f_c_s._t_y_p_e._L_S_R_1_0_2_4 a list of the following options and values: 

_v_e_r_s_i_o_n "2.0"

_b_y_t_e._s_i_z_e 2

_s_i_g_n_e_d TRUE

_e_n_d_i_a_n "auto"

_1_2. _f_c_s._t_y_p_e._f_a_c_s_c_a_n_1_0_2_4 a list of the following options and values: 

_v_e_r_s_i_o_n "2.0"

_b_y_t_e._s_i_z_e 2

_s_i_g_n_e_d TRUE

_e_n_d_i_a_n "auto" 

_V_a_l_u_e:

     With the help of fcs.type, the raw FCS file will be read into a
     FCS R object that can be implemented for further analysis in R.

_A_u_t_h_o_r(_s):

     A.J. Rossini and J.Y. Wan

_R_e_f_e_r_e_n_c_e_s:

     Peter Rabinovitch

_S_e_e _A_l_s_o:

     'read.FCS', 'readBin'

_E_x_a_m_p_l_e_s:

       if (require(rfcdmin)) {
         ## obtaining the location of the fcs files in the data
         get.path<-function(filename) {
           datadir<-system.file("fcs", package="rfcdmin")
           return(paste(datadir, filename, sep="/"))
         }


         FF256 <-read.FCS(get.path("facscan256.fcs"),
                                   fcs.type=fcs.type.facscan256)
       }

