initialization_att1r_projectg

Quarto

library(tidyverse)
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library(here)
here() starts at C:/r_research_outside_of_gdrive/kwan/att1r
library(readxl)
Warning: package 'readxl' was built under R version 4.4.3
library(janitor)
Warning: package 'janitor' was built under R version 4.4.3

Attaching package: 'janitor'

The following objects are masked from 'package:stats':

    chisq.test, fisher.test
library(gtsummary)
Warning: package 'gtsummary' was built under R version 4.4.3

Positive vs non-positive

Characteristic Overall
N = 551		 negative and at risk
N = 431		 positive
N = 121		 p-value2
at1r_interpretation_merged


<0.001
     2 (3.6%) 2 (4.7%) 0 (0%)
    at risk 2 (3.6%) 2 (4.7%) 0 (0%)
    At risk 14 (25%) 14 (33%) 0 (0%)
    negative 4 (7.3%) 4 (9.3%) 0 (0%)
    Negative 21 (38%) 21 (49%) 0 (0%)
    positive 1 (1.8%) 0 (0%) 1 (8.3%)
    Positive 11 (20%) 0 (0%) 11 (92%)
death_sheet_1 18 (39%) 15 (43%) 3 (27%) 0.5
immuno_esc_prolonged 24 (56%) 16 (47%) 8 (89%) 0.055
number_non_hla_positive_beads_sheet_1 4 (1, 12) 4 (1, 8) 17 (12, 28) 0.035
age_of_time_of_sample_sheet_4 75 (68, 79) 75 (68, 78) 77 (73, 81) 0.3
race_sheet_4


0.2
     8 (15%) 7 (16%) 1 (8.3%)
    asian 1 (1.8%) 1 (2.3%) 0 (0%)
    black/aa 6 (11%) 6 (14%) 0 (0%)
    white 39 (71%) 29 (67%) 10 (83%)
    White 1 (1.8%) 0 (0%) 1 (8.3%)
ethnicity_sheet_4


0.3
     8 (15%) 7 (16%) 1 (8.3%)
    hispanic/latinx 1 (1.8%) 0 (0%) 1 (8.3%)
    not hispanic/latinx 46 (84%) 36 (84%) 10 (83%)
metastatic_sheet_4



    1 9 (100%) 8 (100%) 1 (100%)
htn_sheet_4 43 (93%) 33 (94%) 10 (91%) >0.9
hld_sheet_4 37 (80%) 27 (77%) 10 (91%) 0.4
cad_sheet_4 32 (70%) 21 (60%) 11 (100%) 0.020
diabetes_sheet_4 11 (24%) 9 (26%) 2 (18%) >0.9
hf_sheet_4 15 (33%) 10 (29%) 5 (45%) 0.5
valve_sheet_4 3 (6.5%) 2 (5.7%) 1 (9.1%) >0.9
arrhythmia_sheet_4


0.005
     9 (16%) 8 (19%) 1 (8.3%)
    0 27 (49%) 25 (58%) 2 (17%)
    1 18 (33%) 9 (21%) 9 (75%)
    1 (after ICI) 1 (1.8%) 1 (2.3%) 0 (0%)
ipi_sheet_4 13 (28%) 9 (26%) 4 (36%) 0.7
nivo_sheet_4 18 (39%) 14 (40%) 4 (36%) >0.9
pembro_sheet_4 25 (54%) 18 (51%) 7 (64%) 0.5
durva_sheet_4 4 (8.7%) 2 (5.7%) 2 (18%) 0.2
atezo_sheet_4 5 (11%) 4 (11%) 1 (9.1%) >0.9
days_from_initial_exposure_of_ici_to_presentation_sheet_4 82 (39, 446) 67 (35, 276) 505 (78, 1,054) 0.090
pulse_dose_steroids_sheet_4 43 (93%) 34 (97%) 9 (82%) 0.14
steroid_pulse_prolonged 20 (43%) 15 (43%) 5 (45%) >0.9
mmf_sheet_4 23 (50%) 17 (49%) 6 (55%) 0.7
abatacept_sheet_4 16 (35%) 11 (31%) 5 (45%) 0.5
ivig_sheet_4 7 (15%) 4 (11%) 3 (27%) 0.3
infliximab_sheet_4 1 (2.2%) 1 (2.9%) 0 (0%) >0.9
tofacitinib_sheet_4 8 (17%) 8 (23%) 0 (0%) 0.2
immune_suppression_escalation_1_0_sheet_4 23 (49%) 15 (42%) 8 (73%) 0.071
multiple_escalations_sheet_4 1.00 (0.00, 1.00) 0.00 (0.00, 1.00) 1.00 (0.00, 2.00) 0.092
lvef_sheet_4 54 (43, 62) 53 (39, 58) 61 (58, 64) 0.063
rvef_sheet_4 49 (43, 52) 49 (40, 51) 54 (45, 66) 0.14
ischemic_nonischemic_both_sheet_4


>0.9
     28 (61%) 22 (61%) 6 (60%)
    0 1 (2.2%) 1 (2.8%) 0 (0%)
    both 4 (8.7%) 3 (8.3%) 1 (10%)
    nonischemic 13 (28%) 10 (28%) 3 (30%)
other_irae_sheet_4


0.4
     53 (96%) 42 (98%) 11 (92%)
    myositis, MG myocarditis 1 (1.8%) 0 (0%) 1 (8.3%)
    pneumonitis 1 (1.8%) 1 (2.3%) 0 (0%)
t1_52_matt_cmr 1,015 (957, 1,029) 1,015 (992, 1,029) 946 (882, 1,011) 0.10
ecv_matt_cmr 31.0 (26.0, 36.0) 31.0 (27.0, 36.0) 33.0 (26.0, 40.0) 0.7
t2_0_normal1_elevated_matt_cmr 20 (56%) 15 (56%) 5 (56%) >0.9
lge_burden_matt_cmr 6 (0, 10) 5 (0, 8) 11 (4, 15) 0.060
lvef_56_matt_cmr 58 (50, 64) 58 (44, 63) 61 (54, 68) 0.2
rvef_57_matt_cmr 51 (45, 56) 51 (47, 54) 51 (43, 58) 0.5
lv_wall_thickness_ap_matt_cmr 10.00 (8.00, 11.00) 10.00 (8.00, 11.00) 10.00 (6.50, 11.50) 0.9
lv_wall_thickness_pl_matt_cmr 8.00 (7.00, 9.00) 8.00 (6.00, 9.00) 9.00 (7.00, 10.50) 0.12
global_radial_str_matt_cmr 24 (21, 35) 23 (20, 31) 34 (22, 36) 0.2
global_circ_strain_matt_cmr -15.8 (-19.7, -13.6) -15.2 (-19.0, -13.0) -18.4 (-19.8, -14.8) 0.3
gls_matt_cmr -13.9 (-15.8, -10.4) -13.3 (-16.1, -9.1) -14.6 (-15.5, -10.8) 0.6
mapse_anterior_matt_cmr 9.8 (6.3, 12.4) 9.7 (5.9, 12.7) 10.1 (7.3, 12.2) 0.8
mapse_inferior_matt_cmr 11.2 (9.7, 14.4) 12.2 (9.6, 14.6) 10.5 (9.7, 12.9) 0.6
mapse_mean_matt_cmr 10.2 (8.0, 12.5) 10.1 (7.4, 12.7) 10.9 (8.9, 12.0) 0.8
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Wilcoxon rank sum test; NA; Pearson’s Chi-squared test

Negative vs non-negative

Characteristic Overall
N = 551		 negative
N = 251		 positive and at risk
N = 301		 p-value2
at1r_interpretation_merged


<0.001
     2 (3.6%) 0 (0%) 2 (6.7%)
    at risk 2 (3.6%) 0 (0%) 2 (6.7%)
    At risk 14 (25%) 0 (0%) 14 (47%)
    negative 4 (7.3%) 4 (16%) 0 (0%)
    Negative 21 (38%) 21 (84%) 0 (0%)
    positive 1 (1.8%) 0 (0%) 1 (3.3%)
    Positive 11 (20%) 0 (0%) 11 (37%)
death_sheet_1 18 (39%) 8 (38%) 10 (40%) 0.9
immuno_esc_prolonged 24 (56%) 9 (47%) 15 (63%) 0.3
number_non_hla_positive_beads_sheet_1 4 (1, 12) 1 (1, 5) 7 (3, 14) 0.054
age_of_time_of_sample_sheet_4 75 (68, 79) 74 (69, 78) 77 (65, 80) 0.9
race_sheet_4


0.5
     8 (15%) 4 (16%) 4 (13%)
    asian 1 (1.8%) 1 (4.0%) 0 (0%)
    black/aa 6 (11%) 4 (16%) 2 (6.7%)
    white 39 (71%) 16 (64%) 23 (77%)
    White 1 (1.8%) 0 (0%) 1 (3.3%)
ethnicity_sheet_4


>0.9
     8 (15%) 4 (16%) 4 (13%)
    hispanic/latinx 1 (1.8%) 0 (0%) 1 (3.3%)
    not hispanic/latinx 46 (84%) 21 (84%) 25 (83%)
metastatic_sheet_4



    1 9 (100%) 6 (100%) 3 (100%)
htn_sheet_4 43 (93%) 19 (95%) 24 (92%) >0.9
hld_sheet_4 37 (80%) 15 (75%) 22 (85%) 0.5
cad_sheet_4 32 (70%) 13 (65%) 19 (73%) 0.6
diabetes_sheet_4 11 (24%) 5 (25%) 6 (23%) >0.9
hf_sheet_4 15 (33%) 4 (20%) 11 (42%) 0.11
valve_sheet_4 3 (6.5%) 2 (10%) 1 (3.8%) 0.6
arrhythmia_sheet_4


0.5
     9 (16%) 5 (20%) 4 (13%)
    0 27 (49%) 14 (56%) 13 (43%)
    1 18 (33%) 6 (24%) 12 (40%)
    1 (after ICI) 1 (1.8%) 0 (0%) 1 (3.3%)
ipi_sheet_4 13 (28%) 4 (20%) 9 (35%) 0.3
nivo_sheet_4 18 (39%) 7 (35%) 11 (42%) 0.6
pembro_sheet_4 25 (54%) 11 (55%) 14 (54%) >0.9
durva_sheet_4 4 (8.7%) 1 (5.0%) 3 (12%) 0.6
atezo_sheet_4 5 (11%) 2 (10%) 3 (12%) >0.9
days_from_initial_exposure_of_ici_to_presentation_sheet_4 82 (39, 446) 58 (35, 264) 95 (42, 805) 0.3
pulse_dose_steroids_sheet_4 43 (93%) 19 (95%) 24 (92%) >0.9
steroid_pulse_prolonged 20 (43%) 10 (50%) 10 (38%) 0.4
mmf_sheet_4 23 (50%) 11 (55%) 12 (46%) 0.6
abatacept_sheet_4 16 (35%) 8 (40%) 8 (31%) 0.5
ivig_sheet_4 7 (15%) 3 (15%) 4 (15%) >0.9
infliximab_sheet_4 1 (2.2%) 1 (5.0%) 0 (0%) 0.4
tofacitinib_sheet_4 8 (17%) 5 (25%) 3 (12%) 0.3
immune_suppression_escalation_1_0_sheet_4 23 (49%) 8 (38%) 15 (58%) 0.2
multiple_escalations_sheet_4 1.00 (0.00, 1.00) 0.00 (0.00, 1.00) 1.00 (0.00, 1.00) 0.4
lvef_sheet_4 54 (43, 62) 54 (41, 59) 58 (43, 64) 0.5
rvef_sheet_4 49 (43, 52) 46 (39, 50) 50 (45, 58) 0.12
ischemic_nonischemic_both_sheet_4


0.13
     28 (61%) 15 (71%) 13 (52%)
    0 1 (2.2%) 1 (4.8%) 0 (0%)
    both 4 (8.7%) 0 (0%) 4 (16%)
    nonischemic 13 (28%) 5 (24%) 8 (32%)
other_irae_sheet_4


0.7
     53 (96%) 24 (96%) 29 (97%)
    myositis, MG myocarditis 1 (1.8%) 0 (0%) 1 (3.3%)
    pneumonitis 1 (1.8%) 1 (4.0%) 0 (0%)
t1_52_matt_cmr 1,015 (957, 1,029) 1,016 (1,002, 1,027) 964 (938, 1,069) 0.3
ecv_matt_cmr 31.0 (26.0, 36.0) 33.0 (27.0, 36.0) 31.0 (26.0, 34.0) >0.9
t2_0_normal1_elevated_matt_cmr 20 (56%) 10 (56%) 10 (56%) >0.9
lge_burden_matt_cmr 6 (0, 10) 5 (0, 8) 7 (3, 12) 0.060
lvef_56_matt_cmr 58 (50, 64) 60 (53, 63) 58 (47, 65) >0.9
rvef_57_matt_cmr 51 (45, 56) 52 (49, 54) 50 (40, 58) 0.5
lv_wall_thickness_ap_matt_cmr 10.00 (8.00, 11.00) 10.00 (8.00, 11.00) 11.00 (8.00, 12.00) 0.10
lv_wall_thickness_pl_matt_cmr 8.00 (7.00, 9.00) 7.00 (6.00, 9.00) 8.00 (7.00, 10.00) 0.088
global_radial_str_matt_cmr 24 (21, 35) 29 (22, 33) 23 (20, 36) 0.6
global_circ_strain_matt_cmr -15.8 (-19.7, -13.6) -17.8 (-19.9, -14.5) -15.1 (-19.6, -13.5) 0.4
gls_matt_cmr -13.9 (-15.8, -10.4) -14.9 (-16.7, -12.1) -11.2 (-14.9, -9.1) 0.042
mapse_anterior_matt_cmr 9.8 (6.3, 12.4) 10.4 (6.1, 13.9) 9.4 (7.2, 11.7) 0.3
mapse_inferior_matt_cmr 11.2 (9.7, 14.4) 12.5 (10.1, 14.6) 10.5 (8.4, 12.9) 0.2
mapse_mean_matt_cmr 10.2 (8.0, 12.5) 12.2 (9.3, 13.6) 9.2 (7.7, 12.0) 0.094
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Pearson’s Chi-squared test; Wilcoxon rank sum test; NA

Removed all “at risk”