01_chmi_aim1.md

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

info for aim_1

data subset

• Filters:
• 1st step: dataset != 'T2' or status_ori != naive.

general summary

> dat_1 <- chmi.phen(
    data_type = 'ab_data',
    aim_data = 'aim_1',
    fold_change = FALSE,
    group_tr = 'ab_select')

> summary(dat_1)

  original_id    dataset    gender           immune_status_ori  ppp_time                  status_ori         antigen        log10_mfi         mfi_corr          t_igg     
 L1_002 :  610   L1:13542   F:12200   naive           : 7564   Min.   : 7.00   naive           : 7564   ama1_3d71: 1578   Min.   :0.7193   Min.   :        5   IgG :5523  
 L1_007 :  610   T1: 5368   M:19886   semi_immune     :11346   1st Qu.:12.28   PfSPZ_vaccinated:13176   ama1_fvo : 1578   1st Qu.:3.2221   1st Qu.:     1668   IgG1:5523  
 L1_009 :  610   T2:13176             vaccinated_12800: 4392   Median :15.97   semi_immune     :11346   cel_tos  : 1578   Median :4.3799   Median :    23980   IgG2:5523  
 L1_010 :  610                        vaccinated_3200 : 4392   Mean   :16.07                            csp      : 1578   Mean   :4.3657   Mean   :  4837107   IgG3:5260  
 L1_011 :  610                        vaccinated_51200: 4392   3rd Qu.:21.00                            cy_rpa1  : 1578   3rd Qu.:5.6801   3rd Qu.:   478715   IgG4:4734  
 L1_013 :  610                                                 Max.   :24.89                            cy_rpa2  : 1578   Max.   :8.8091   Max.   :644245615   IgM :5523  
 (Other):28426                                                 NA's   :4880                             (Other)  :22618                                                   
 t_point       t2_point   
 C_1:7320   C_1    :7320  
 D13:2806   D11_D13:7198  
 D19:2318   D19    :2318  
 D28:3621   D28    :3621  
 D7 :7320   D7     :7320  
 D84:4309   D84    :4309  
 DM :4392  

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