02_chmi_aim2.md

In mvazquezs/chmitools: Package to manage & obtain results of the CHMI Study

info for aim_2

data subset

• 1st filter: datasset == 'T2' (only TUCHMI-2 Study).

general summary

> dat_2 <- chmi.phen(
    data_type = 'ab_data',
    aim_data = 'aim_2',
    fold_change = FALSE,
    group_tr = 'ab_select')

> summary(dat_2)

  original_id    dataset    gender          immune_status_ori  ppp_time                  status_ori                vaccine          antigen        log10_mfi     
 T2_002 :  488   T2:17080   F:8296   naive           :3904    Min.   :10.78   PfSPZ_vaccinated:13176   placebo         :3904   ama1_3d71:  840   Min.   :0.7193  
 T2_006 :  488              M:8784   vaccinated_12800:4392    1st Qu.:12.00   NA's            : 3904   semi_immune     :   0   ama1_fvo :  840   1st Qu.:2.9664  
 T2_007 :  488                       vaccinated_3200 :4392    Median :21.00                            vaccinated_3200 :4392   cel_tos  :  840   Median :3.9733  
 T2_010 :  488                       vaccinated_51200:4392    Mean   :16.93                            vaccinated_12800:4392   csp      :  840   Mean   :4.0613  
 T2_011 :  488                                                3rd Qu.:21.00                            vaccinated_51200:4392   cy_rpa1  :  840   3rd Qu.:5.4155  
 T2_012 :  488                                                Max.   :21.00                                                    cy_rpa2  :  840   Max.   :8.6363  
 (Other):14152                                                                                                                 (Other)  :12040                   
    mfi_corr          t_igg      t_point       t2_point   
 Min.   :        5   IgG :2940   C_1:4270   C_1    :4270  
 1st Qu.:      926   IgG1:2940   D7 :4270   D11_D13:4270  
 Median :     9403   IgG2:2940   D84:4270   D7     :4270  
 Mean   :  1081489   IgG3:2800   DM :4270   D84    :4270  
 3rd Qu.:   260339   IgG4:2520                            
 Max.   :432849806   IgM :2940

mvazquezs/chmitools documentation built on May 1, 2020, 2:06 a.m.