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 = 471		 negative and at risk
N = 361		 positive
N = 111		 p-value2
at1r_interpretation_merged


<0.001
    at risk 2 (4.3%) 2 (5.6%) 0 (0%)
    At risk 11 (23%) 11 (31%) 0 (0%)
    negative 4 (8.5%) 4 (11%) 0 (0%)
    Negative 19 (40%) 19 (53%) 0 (0%)
    positive 1 (2.1%) 0 (0%) 1 (9.1%)
    Positive 10 (21%) 0 (0%) 10 (91%)
death_sheet_1 15 (33%) 13 (37%) 2 (18%) 0.3
immuno_esc_prolonged 25 (58%) 17 (50%) 8 (89%) 0.057
number_non_hla_positive_beads_sheet_1 4 (1, 12) 4 (1, 8) 23 (15, 29) 0.004
age_of_time_of_sample_sheet_4 74 (68, 78) 74 (67, 78) 77 (73, 81) 0.2
race_sheet_4


0.2
    black/aa 5 (11%) 5 (14%) 0 (0%)
    white 41 (87%) 31 (86%) 10 (91%)
    White 1 (2.1%) 0 (0%) 1 (9.1%)
gender_1_female 0 (NA%) 0 (NA%) 0 (NA%)
ethnicity_sheet_4


0.2
    hispanic/latinx 1 (2.1%) 0 (0%) 1 (9.1%)
    not hispanic/latinx 46 (98%) 36 (100%) 10 (91%)
metastatic_sheet_4 11 (79%) 9 (75%) 2 (100%) >0.9
htn_sheet_4 43 (93%) 34 (97%) 9 (82%) 0.14
hld_sheet_4 37 (80%) 27 (77%) 10 (91%) 0.4
cad_sheet_4 28 (61%) 18 (51%) 10 (91%) 0.032
diabetes_sheet_4 10 (22%) 9 (26%) 1 (9.1%) 0.4
hf_sheet_4 15 (33%) 11 (31%) 4 (36%) >0.9
valve_sheet_4 2 (4.3%) 2 (5.7%) 0 (0%) >0.9
ipi_sheet_4 11 (24%) 7 (20%) 4 (36%) 0.4
nivo_sheet_4 16 (35%) 12 (34%) 4 (36%) >0.9
pembro_sheet_4 25 (54%) 18 (51%) 7 (64%) 0.5
durva_sheet_4 5 (11%) 3 (8.6%) 2 (18%) 0.6
atezo_sheet_4 6 (13%) 5 (14%) 1 (9.1%) >0.9
days_from_initial_exposure_of_ici_to_presentation_sheet_4 75 (33, 333) 57 (33, 194) 145 (50, 1,009) 0.15
pulse_dose_steroids_sheet_4 42 (93%) 33 (97%) 9 (82%) 0.14
steroid_pulse_prolonged 22 (49%) 16 (47%) 6 (55%) 0.7
mmf_sheet_4 25 (56%) 19 (56%) 6 (55%) >0.9
abatacept_sheet_4 17 (38%) 13 (38%) 4 (36%) >0.9
ivig_sheet_4 10 (22%) 6 (18%) 4 (36%) 0.2
infliximab_sheet_4 2 (4.4%) 2 (5.9%) 0 (0%) >0.9
tofacitinib_sheet_4 11 (24%) 10 (29%) 1 (9.1%) 0.2
immune_suppression_escalation_1_0_sheet_4 25 (54%) 17 (49%) 8 (73%) 0.2
multiple_escalations_sheet_4 1.00 (0.00, 1.00) 0.50 (0.00, 1.00) 1.00 (0.00, 2.00) 0.2
lvef_sheet_4 58 (48, 63) 54 (39, 61) 64 (58, 64) 0.036
rvef_sheet_4 49 (45, 56) 49 (44, 52) 58 (50, 66) 0.078
ischemic_nonischemic_both_sheet_4


0.6
     24 (62%) 18 (60%) 6 (67%)
    0 1 (2.6%) 1 (3.3%) 0 (0%)
    both 2 (5.1%) 1 (3.3%) 1 (11%)
    nonischemic 12 (31%) 10 (33%) 2 (22%)
other_irae_sheet_4


0.4
     45 (96%) 35 (97%) 10 (91%)
    myositis, MG myocarditis 1 (2.1%) 0 (0%) 1 (9.1%)
    pneumonitis 1 (2.1%) 1 (2.8%) 0 (0%)
t1_52_matt_cmr 1,014 (957, 1,029) 1,015 (992, 1,029) 946 (882, 1,011) 0.10
ecv_matt_cmr


0.6
    21 1 (10%) 1 (13%) 0 (0%)
    23 1 (10%) 1 (13%) 0 (0%)
    26 1 (10%) 0 (0%) 1 (50%)
    27 1 (10%) 1 (13%) 0 (0%)
    31 1 (10%) 1 (13%) 0 (0%)
    34 1 (10%) 1 (13%) 0 (0%)
    36 2 (20%) 2 (25%) 0 (0%)
    38 1 (10%) 1 (13%) 0 (0%)
    40 1 (10%) 0 (0%) 1 (50%)
t2_0_normal1_elevated_matt_cmr 20 (63%) 15 (63%) 5 (63%) >0.9
lge_burden_matt_cmr 7 (3, 11) 5 (0, 9) 11 (4, 15) 0.037
cm_outcome



    1 14 (100%) 12 (100%) 2 (100%)
lvef_56_matt_cmr 58 (52, 64) 58 (44, 63) 64 (58, 68) 0.10
rvef_57_matt_cmr 52 (48, 57) 52 (48, 54) 52 (45, 58) 0.4
lv_wall_thickness_ap_matt_cmr 10.00 (8.00, 11.00) 10.00 (8.00, 11.00) 9.00 (6.00, 11.00) 0.7
lv_wall_thickness_pl_matt_cmr 8.00 (7.00, 9.00) 7.50 (6.00, 9.00) 9.00 (7.00, 11.00) 0.12
global_radial_str_matt_cmr 25 (21, 36) 23 (20, 31) 34 (22, 36) 0.3
global_circ_strain_matt_cmr -15.9 (-19.9, -13.9) -15.2 (-19.9, -13.5) -18.4 (-19.8, -14.8) 0.4
gls_matt_cmr -13.9 (-16.1, -10.8) -13.3 (-16.6, -10.0) -14.6 (-15.5, -10.8) 0.7
abnormal_gls 33 (85%) 24 (86%) 9 (82%) >0.9
mapse_anterior_matt_cmr 10.0 (7.3, 12.4) 9.8 (6.3, 13.4) 10.1 (7.3, 12.2) >0.9
mapse_inferior_matt_cmr 11.7 (9.8, 14.5) 12.2 (9.8, 14.6) 10.5 (9.7, 12.9) 0.5
mapse_mean_matt_cmr 10.6 (8.6, 12.5) 10.2 (8.5, 12.8) 10.9 (8.9, 12.0) >0.9
remove_variavle NA (NA, NA) NA (NA, NA) NA (NA, NA)
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 = 471		 negative
N = 231		 positive and at risk
N = 241		 p-value2
at1r_interpretation_merged


<0.001
    at risk 2 (4.3%) 0 (0%) 2 (8.3%)
    At risk 11 (23%) 0 (0%) 11 (46%)
    negative 4 (8.5%) 4 (17%) 0 (0%)
    Negative 19 (40%) 19 (83%) 0 (0%)
    positive 1 (2.1%) 0 (0%) 1 (4.2%)
    Positive 10 (21%) 0 (0%) 10 (42%)
death_sheet_1 15 (33%) 9 (39%) 6 (26%) 0.3
immuno_esc_prolonged 25 (58%) 10 (48%) 15 (68%) 0.2
number_non_hla_positive_beads_sheet_1 4 (1, 12) 1 (1, 5) 10 (4, 16) 0.024
age_of_time_of_sample_sheet_4 74 (68, 78) 74 (69, 78) 75 (65, 79) >0.9
race_sheet_4


0.3
    black/aa 5 (11%) 4 (17%) 1 (4.2%)
    white 41 (87%) 19 (83%) 22 (92%)
    White 1 (2.1%) 0 (0%) 1 (4.2%)
gender_1_female 0 (NA%) 0 (NA%) 0 (NA%)
ethnicity_sheet_4


>0.9
    hispanic/latinx 1 (2.1%) 0 (0%) 1 (4.2%)
    not hispanic/latinx 46 (98%) 23 (100%) 23 (96%)
metastatic_sheet_4 11 (79%) 6 (67%) 5 (100%) 0.3
htn_sheet_4 43 (93%) 22 (100%) 21 (88%) 0.2
hld_sheet_4 37 (80%) 16 (73%) 21 (88%) 0.3
cad_sheet_4 28 (61%) 13 (59%) 15 (63%) 0.8
diabetes_sheet_4 10 (22%) 7 (32%) 3 (13%) 0.2
hf_sheet_4 15 (33%) 7 (32%) 8 (33%) >0.9
valve_sheet_4 2 (4.3%) 2 (9.1%) 0 (0%) 0.2
ipi_sheet_4 11 (24%) 3 (14%) 8 (33%) 0.12
nivo_sheet_4 16 (35%) 6 (27%) 10 (42%) 0.3
pembro_sheet_4 25 (54%) 13 (59%) 12 (50%) 0.5
durva_sheet_4 5 (11%) 2 (9.1%) 3 (13%) >0.9
atezo_sheet_4 6 (13%) 3 (14%) 3 (13%) >0.9
days_from_initial_exposure_of_ici_to_presentation_sheet_4 75 (33, 333) 67 (35, 239) 75 (31, 594) 0.8
pulse_dose_steroids_sheet_4 42 (93%) 20 (95%) 22 (92%) >0.9
steroid_pulse_prolonged 22 (49%) 11 (52%) 11 (46%) 0.7
mmf_sheet_4 25 (56%) 13 (62%) 12 (50%) 0.4
abatacept_sheet_4 17 (38%) 9 (43%) 8 (33%) 0.5
ivig_sheet_4 10 (22%) 4 (19%) 6 (25%) 0.7
infliximab_sheet_4 2 (4.4%) 2 (9.5%) 0 (0%) 0.2
tofacitinib_sheet_4 11 (24%) 6 (29%) 5 (21%) 0.5
immune_suppression_escalation_1_0_sheet_4 25 (54%) 10 (45%) 15 (63%) 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 58 (48, 63) 54 (41, 59) 58 (48, 64) 0.2
rvef_sheet_4 49 (45, 56) 46 (39, 50) 52 (49, 63) 0.015
ischemic_nonischemic_both_sheet_4


0.4
     24 (62%) 13 (68%) 11 (55%)
    0 1 (2.6%) 1 (5.3%) 0 (0%)
    both 2 (5.1%) 0 (0%) 2 (10%)
    nonischemic 12 (31%) 5 (26%) 7 (35%)
other_irae_sheet_4


>0.9
     45 (96%) 22 (96%) 23 (96%)
    myositis, MG myocarditis 1 (2.1%) 0 (0%) 1 (4.2%)
    pneumonitis 1 (2.1%) 1 (4.3%) 0 (0%)
t1_52_matt_cmr 1,014 (957, 1,029) 1,015 (992, 1,029) 964 (938, 1,069) 0.3
ecv_matt_cmr


0.4
    21 1 (10%) 1 (20%) 0 (0%)
    23 1 (10%) 0 (0%) 1 (20%)
    26 1 (10%) 0 (0%) 1 (20%)
    27 1 (10%) 1 (20%) 0 (0%)
    31 1 (10%) 0 (0%) 1 (20%)
    34 1 (10%) 0 (0%) 1 (20%)
    36 2 (20%) 2 (40%) 0 (0%)
    38 1 (10%) 1 (20%) 0 (0%)
    40 1 (10%) 0 (0%) 1 (20%)
t2_0_normal1_elevated_matt_cmr 20 (63%) 10 (59%) 10 (67%) 0.6
lge_burden_matt_cmr 7 (3, 11) 5 (0, 8) 9 (4, 13) 0.070
cm_outcome



    1 14 (100%) 6 (100%) 8 (100%)
lvef_56_matt_cmr 58 (52, 64) 59 (53, 63) 58 (50, 68) 0.5
rvef_57_matt_cmr 52 (48, 57) 52 (48, 54) 50 (45, 58) >0.9
lv_wall_thickness_ap_matt_cmr 10.00 (8.00, 11.00) 10.00 (7.00, 11.00) 11.00 (8.00, 11.00) 0.2
lv_wall_thickness_pl_matt_cmr 8.00 (7.00, 9.00) 7.00 (6.00, 9.00) 8.00 (7.00, 10.00) 0.13
global_radial_str_matt_cmr 25 (21, 36) 29 (22, 36) 23 (21, 36) 0.9
global_circ_strain_matt_cmr -15.9 (-19.9, -13.9) -17.8 (-20.3, -13.0) -15.2 (-19.6, -14.2) 0.8
gls_matt_cmr -13.9 (-16.1, -10.8) -14.8 (-17.3, -11.7) -12.1 (-15.1, -9.6) 0.15
abnormal_gls 33 (85%) 15 (83%) 18 (86%) >0.9
mapse_anterior_matt_cmr 10.0 (7.3, 12.4) 10.4 (6.1, 13.9) 9.7 (7.3, 11.7) 0.5
mapse_inferior_matt_cmr 11.7 (9.8, 14.5) 12.5 (10.1, 14.6) 10.6 (8.9, 13.3) 0.2
mapse_mean_matt_cmr 10.6 (8.6, 12.5) 12.2 (9.3, 13.6) 10.0 (8.6, 12.0) 0.3
remove_variavle NA (NA, NA) NA (NA, NA) NA (NA, NA)
1 n (%); Median (Q1, Q3)
2 Fisher’s exact test; Pearson’s Chi-squared test; Wilcoxon rank sum test; NA

Removed all “at risk”