PerPosROCmin             package:rfcdmin             R Documentation

_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 _d_a_t_a-_P_e_r_c_e_n_t_a_g_e
_P_o_s_i_t_i_v_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     Note: Percentage Positives = 100*(Percent Positives) of the
     stimulated sample based on the 99.9th percentile of the
     unstimulated distribution.

     For each sample/individual of the Interferon Gamma variable
     (cytokine repsonses), a 100*percent positive is defined as 100*
     the ratio of GAG stimulated cells greater than the 99.9th
     percentile of corresponding sample of unstimulated cells' (from
     the same given individual) distribution over the total number of
     GAG stimulated cells in the given sample from the individual.

     Thus, for a given individual, 100*Percent Positive = 100*k/n,
     where k is the number of stimulated cells >= 99.9th percentile of
     the corresponding distribution of the unstimulated cells of the
     same individual and n is the total number of stimulated cells in
     the sample.

     The following are the 100*(percent positives) for different
     peptide stimulations (GAG, PolA, or PolB) and different
     individuals (HIV positive & HIV negative).

     _h_i_v_p_o_s._g_a_g 100*(Percent Positives) of the GAG stimulated cells
          from 29 HIV positive individuals

     _h_i_v_n_e_g._g_a_g 100*(Percent Positives) of the GAG stimulated cells
          from 10 HIV negative individuals

     _h_i_v_p_o_s._p_o_l_a 100*(Percent Positives) of the PolA stimulated cells
          from 29 HIV positive individuals

     _h_i_v_n_e_g._p_o_l_a 100*(Percent Positives) of the PolA stimulated cells
          from 10 HIV negative individuals 

     _h_i_v_p_o_s._p_o_l_b 100*(Percent Positives) of the PolB stimulated cells
          from 29 HIV positive individuals 

     _h_i_v_n_e_g._p_o_l_b 100*(Percent Positives) of the PolB stimulated cells
          from 10 HIV negative individuals  

_U_s_a_g_e:

      data(PerPosROC)

_F_o_r_m_a_t:

     Four numeric vectors

_S_o_u_r_c_e:

     Cytokine reponse Table from Zoe Moodie PhD who obtained the
     percent positives from the data from the Vaccine Research Center
     (VRC), NIH, Bethesda, MD

     Also from the 'PerPosROC' data from the 'rfcdorig' data package.

_E_x_a_m_p_l_e_s:

        data(PerPosROCmin)
     if (require(rflowcyt)){
     ## the example below comes from ROC.FCS function

     #plotting the gag stimulated 100* percent positives
        if (interactive()==TRUE){
           GAG<-ROC.FCS(hivpos.gag, hivneg.gag)
     #plotting the pola stimulated 100* percent positives
           POLA<-ROC.FCS(hivpos.pola, hivneg.pola, lineopt=2, colopt=2, overlay=TRUE)
     #plotting the polb stimulated 100* percent positives
           POLB<-ROC.FCS(hivpos.polb, hivneg.polb, lineopt=4, colopt=3, overlay=TRUE)
           legend(0.7, 0.7, c("gag", "polA", "polB"), col = c(1,2,3), lty=c(1,2,4))
         }
     } else {
     cat("Installation of the rflowcyt package is needed to run the examples.", "\n\n")
     }

