04_chmi_aim4.md

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

info for aim_4

data subset

regression models table for the aim_4

To summarise the info about regressions models for each question in the aim_4 (see 20.02.06_chmi_aim4 table).

general summary

> dat_4 <- chmi.phen(
        data_type = 'ab_data',
        aim_data = 'aim_4',
        fold_change = FALSE,
        group_tr = 'ab_select')

> summary(dat_4)

  original_id    dataset    gender    hb_status_ori        immune_status_ori      mal_exposure   pcr_pos_pid  ppp_tbs         ppp_time                  status_ori   
 L1_002 :  610   L1:13542   F:15616   AA:30866      naive           :11468   naive      : 7564   0:11224     Min.   : 0.00   Min.   : 7.00   naive           : 7564  
 L1_007 :  610   T1: 5368   M:20374   AS: 5124      semi_immune     :11346   placebo    :    0   1:24766     1st Qu.:11.00   1st Qu.:11.91   PfSPZ_vaccinated:13176  
 L1_009 :  610   T2:17080                           vaccinated_12800: 4392   semi_immune:11346               Median :12.00   Median :14.71   semi_immune     :11346  
 L1_010 :  610                                      vaccinated_3200 : 4392   vaccinated :13176               Mean   :12.99   Mean   :15.63   NA's            : 3904  
 L1_011 :  610                                      vaccinated_51200: 4392   NA's       : 3904               3rd Qu.:17.00   3rd Qu.:21.00                           
 L1_013 :  610                                                                                               Max.   :28.00   Max.   :24.89                           
 (Other):32330                                                                                               NA's   :976     NA's   :4880                            
       t_immuno_ori   tbs_pos_qpcr      antigen        log10_mfi         mfi_corr          t_igg      t_point       t2_point   
 asymptomatic: 5124   0:13664      ama1_3d71: 1770   Min.   :0.7193   Min.   :        5   IgG :6195   C_1:8296   C_1    :8296  
 naive       : 2196   1:22326      ama1_fvo : 1770   1st Qu.:3.1698   1st Qu.:     1478   IgG1:6195   D13:2806   D11_D13:8174  
 sterile     : 2440                cel_tos  : 1770   Median :4.3011   Median :    20004   IgG2:6195   D19:2318   D19    :2318  
 symptomatic : 3782                csp      : 1770   Mean   :4.3110   Mean   :  4354081   IgG3:5900   D28:3621   D28    :3621  
 NA's        :22448                cy_rpa1  : 1770   3rd Qu.:5.6371   3rd Qu.:   433655   IgG4:5310   D7 :8296   D7     :8296  
                                   cy_rpa2  : 1770   Max.   :8.8091   Max.   :644245615   IgM :6195   D84:5285   D84    :5285  
                                   (Other)  :25370                                                    DM :5368  

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