FHCRC.HVTNFCS            package:rflowcyt            R Documentation

_F_r_e_d _H_u_t_c_h_i_n_s_o_n _C_a_n_c_e_r _R_e_s_e_a_r_c_h _C_e_n_t_e_r _S_e_q_u_e_n_t_i_a_l _G_a_t_i_n_g
_P_r_o_c_e_d_u_r_e _p_r_o_p_o_s_e_d _b_y _J_u_l_i_e _M_c_E_l_r_a_t_h'_s _L_a_b

_D_e_s_c_r_i_p_t_i_o_n:

     This function uses 'icreateGate' and 'createGate' to select the
     datapoints which are of particular interest.  The selection
     process is realized in an index column which is added to the data
     of the FCS object.  In particular, after a series of
     gating/datapoint selection sequences, the interferon gamma
     variable is of interest.

     To row reduce the data of the FCS object, the function,
     'extractGatedData' should be used on the last gate index to obtain
     the rows/cells and then should be used again to subset across
     columns to obtain the gamma interferon column.

_U_s_a_g_e:

     FHCRC.HVTNFCS(myFCSobj, gate1.vars = c(1, 2), gate2.vars = c(5, 7),
                      gate3.vars = c(3, 4),MY.DEBUG = FALSE)

_A_r_g_u_m_e_n_t_s:

myFCSobj: a FCS object

gate1.vars: The vector of column variable positions corresponding to
          Forward Scatter and Side Scatter variables for the first
          gate; default is column positions 1 and 2 respectively

gate2.vars: The vector of column variable positions corresponding to
          cd3 and cd8 variables for the second gate; default is column
          positions 5 and 7 respectively

gate3.vars: The vector of column variable positions corresponding to
          cd69 and Interferon Gamma variables for gate 3; default is
          column positions 3 and 4 respectively

MY.DEBUG: if TRUE, then will print the debugging statements; otherwise,
          if FALSE, then will surpress the debugging statements;
          default is FALSE

_D_e_t_a_i_l_s:

     The Selection Sequence made by Julie McElrath's Lab is the
     following:

*_g_a_t_e_1:_b_i_d_c_u_t:* Forward Scatter VS Side Scatter

_s_i_n_g_l_e _g_a_t_e  (Select the lymphocytes-central cluster) 

*_g_a_t_e_2:_b_i_d_c_u_t:* cd3 VS cd8

_g_a_t_e _2._1: (Select cd3+/cd8-)

_g_a_t_e _2._2: (Select cd3+/cd8+)

*_g_a_t_e_3:_b_i_s_c_u_t:* cd69 vs Interferon Gamma

_g_a_t_e _3._1: (Select +/+ which are the cd4+ cells (from gate2.1))

_g_a_t_e _3._2: (Select +/+ which are the cd8+ cells (from gate2.2))

     In General, the types of Gating/Cutting that are used in this
     gating scheme are the following:

_u_n_i_s_c_u_t = _u_n_i_v_a_r_i_a_t_e _s_i_n_g_l_e _c_u_t (Selection of the positive/right half)

_b_i_s_c_u_t = _b_i_v_a_r_i_a_t_e _s_i_n_g_l_e _c_u_t (Selection of the +/-, -/-. +/+, or -/+
     quadrant)

_b_i_d_c_u_t = _b_i_v_a_r_i_a_t_e _d_o_u_b_l_e _c_u_t (Selection of the center rectangle that
     results)

_V_a_l_u_e:

FCS object: with the following slots:

    data: A augmented dataframe with the added-on gating column
          variables/indices

metadata: a FCSmetadata object with the information about the gating
          column variables: $PnR (gating range), $PnN (gating
          variable's shortname/unused name in the data of the FCS
          object), $PnS (gating variable's longname/used name), and
          other slot information

_W_A_R_N_I_N_G:

     This gating scheme is not standard, and there may have been
     changes to the gating scheme.  This gating scheme only serves as
     an example, which demonstrates the use of
     'createGate','icreateGate' and '"[[-methods"' which extracts the
     metadata information (eg. in order to obatin information about a
     previous gating index/column variable

_N_o_t_e:

     The "FHCRC" data from the 'rfcdorig' package can be used for this
     sequential gating scheme.

_A_u_t_h_o_r(_s):

     A.J. Rossini and J.Y. Wan

_R_e_f_e_r_e_n_c_e_s:

     Julie McElrath, PhD

_S_e_e _A_l_s_o:

     'createGate', 'icreateGate', 'showgate.FCS', 'VRC.HVTNFCS',
     'plotvar.FCS', '"[-methods"', '"[[-methods"'

_E_x_a_m_p_l_e_s:

       if (require(rfcdmin)){

         data.there<-is.element("MC.053",objects())
         if ( ( sum(data.there) != length(data.there) )){
           ## obtaining the FCS objects from VRC data
           data(MC.053min)
         }

         if (interactive()==TRUE){
           par(mfrow=c(4,2))

           MC.053.FHCRC<-FHCRC.HVTNFCS(MC.053)
         }
       }

