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")
     }

