VRC.HVTNFCS             package:rflowcyt             R Documentation

_S_e_q_u_e_n_t_i_a_l _G_a_t_i_n_g _S_c_h_e_m_e _f_r_o_m _V_a_c_c_i_n_e _R_e_s_e_a_r_c_h _C_e_n_t_e_r
(_V_R_C), _N_I_H, _B_e_t_h_e_s_d_a, _M_D; _M_a_r_i_o _R_o_e_d_e_r_e_r, _P_h_D

_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:

     VRC.HVTNFCS(myFCSobj, gate1.vars = c(1, 2), gate2.vars = c(7, 5),
                      gate3.vars = c(5, 3),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 cd4 variables for the second gate; default is column
          positions 7 and 5 respectively

gate3.vars: The vector of column variable positions corresponding to
          cd4 and cd8 variables for gate 3; default is column positions
          5 and 3 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 proposed by Mario Roederer is the
     following:

*_g_a_t_e_1:_b_i_p_c_u_t:* Forward Scatter VS Side Scatter (Select the
     lymphocytes-central cluster) 

*_g_a_t_e_2:_b_i_d_c_u_t:* cd3 VS cd4 (want cd3+ cells) (Select the cd3 positive
     cells on the right of the cutoff)

*_g_a_t_e_3:_b_i_s_c_u_t:* cd4 vs cd8  gate 3.1: (Select cd4+/cd8- cells)  (+/-
     quadrant) gate 3.2: (Select cd4-/cd8+ cells)  (-/+ quadrant)

     In General, Types of Gating/Cutting:

_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 'extractGateHistory' which extracts
     the gating information (eg. in order to obtain information about a
     previous gating index/column variable)

_N_o_t_e:

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

_A_u_t_h_o_r(_s):

     A.J. Rossini & J.Y. Wan

_R_e_f_e_r_e_n_c_e_s:

     Mario Roederer, PhD

_S_e_e _A_l_s_o:

     'createGate', 'icreateGate', 'FHCRC.HVTNFCS', 'plotvar.FCS',
     'extractGatedData', 'extractGateHistory'

_E_x_a_m_p_l_e_s:

     if (require(rfcdmin)){

     data.there<-is.element(c("st.1829", "unst.1829", "st.DRT", "unst.DRT"),objects())
     if ( ( sum(data.there) != length(data.there) )){
     ## obtaining the FCS objects from VRC data
     data(VRCmin)
     }



     # HIV positive individual
     if (interactive()==TRUE){
     par(mfrow=c(4,2))
     st.DRT.VRC<-VRC.HVTNFCS(st.DRT)
     }

     }

