Lamis_project
Mst Afroza Parvin
9/27/2022
## New names:
## * `` -> ...8
## * `` -> ...9
## * `` -> ...11
## * `` -> ...12
## * `` -> ...13
## * ...## # A tibble: 6 x 22
## age symptom `T cells (CD3)` `T helper cells (CD… `T cytotoxic cells (…
## <dbl> <chr> <chr> <chr> <chr>
## 1 57 autoimmun… 393.10650000000… 29.070900000000005 388.11150000000004
## 2 36 infection 1227.5200000000… 716.80000000000007 614.65600000000006
## 3 0.25 infection 7.0355999999999… 6.8639999999999999 0.17160000000000003
## 4 0.25 infection 5.1072000000000… 0.10639999999999999 1.3832
## 5 0.0904 infection 180.75000000000… 97.5 16.95
## 6 4 infection 1311.0519999999… 946.12000000000012 247.00490000000002
## # … with 17 more variables: (CD4 -ve/CD8 -ve) T cells / % <dbl>,
## # (CD4+ve/CD8 +ve) T cells / % <dbl>, ...8 <dbl>, ...9 <dbl>,
## # CD25 T-helper cells <dbl>, ...11 <dbl>, ...12 <dbl>, ...13 <lgl>,
## # ...14 <lgl>, CD4:CD8 Ratio <dbl>, B cells (CD19) <dbl>,
## # NK cells (CD16) <chr>, CD4/CD45RO cells <dbl>, ...19 <dbl>, ...20 <lgl>,
## # ...21 <lgl>, ...22 <dbl>## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
## Warning: NAs introduced by coercion
| Characteristics | autoimmunity (N=28) |
diarrhea (N=20) |
infection (N=71) |
lymphoproliferation (N=20) |
Total (N=139) |
|---|---|---|---|---|---|
| T cells (CD3) | |||||
| Mean (SD) | 1610 (1330) | 2540 (1190) | 1130 (1040) | 3590 (2190) | 1780 (1590) |
| Median [Min, Max] | 1130 [393, 6340] | 2750 [730, 5700] | 891 [3.00, 4580] | 2870 [189, 8490] | 1270 [3.00, 8490] |
| Missing | 1 (3.6%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (0.7%) |
| T helper cells (CD3/CD4) | |||||
| Mean (SD) | 592 (350) | 1390 (731) | 558 (587) | 1990 (1300) | 892 (891) |
| Median [Min, Max] | 481 [29.1, 1510] | 1240 [320, 2790] | 447 [0, 2680] | 1610 [82.0, 4730] | 626 [0, 4730] |
| Missing | 1 (3.6%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (0.7%) |
| T cytotoxic cells (CD3/CD8) | |||||
| Mean (SD) | 845 (874) | 997 (806) | 463 (464) | 1330 (1210) | 741 (806) |
| Median [Min, Max] | 474 [176, 3940] | 734 [270, 3800] | 303 [0.172, 2000] | 954 [80.0, 5540] | 517 [0.172, 5540] |
| Missing | 2 (7.1%) | 0 (0%) | 0 (0%) | 0 (0%) | 2 (1.4%) |
| CD25 T-helper cells | |||||
| Mean (SD) | 212 (NA) | NA (NA) | NA (NA) | NA (NA) | 212 (NA) |
| Median [Min, Max] | 212 [212, 212] | NA [NA, NA] | NA [NA, NA] | NA [NA, NA] | 212 [212, 212] |
| Missing | 27 (96.4%) | 20 (100%) | 71 (100%) | 20 (100%) | 138 (99.3%) |
| CD4:CD8 Ratio | |||||
| Mean (SD) | 1.23 (1.18) | 1.55 (0.874) | 2.42 (5.27) | 1.47 (0.654) | 1.94 (3.92) |
| Median [Min, Max] | 0.933 [0.0749, 5.38] | 1.23 [0.548, 3.20] | 1.10 [0, 40.0] | 1.26 [0.472, 2.99] | 1.16 [0, 40.0] |
| Missing | 3 (10.7%) | 3 (15.0%) | 4 (5.6%) | 3 (15.0%) | 13 (9.4%) |
| B cells (CD19) | |||||
| Mean (SD) | 990 (1150) | 298 (216) | 495 (713) | 1670 (1970) | 732 (1120) |
| Median [Min, Max] | 634 [8.00, 5610] | 266 [13.0, 750] | 214 [0, 4380] | 915 [42.0, 8060] | 358 [0, 8060] |
| Missing | 2 (7.1%) | 0 (0%) | 4 (5.6%) | 1 (5.0%) | 7 (5.0%) |
| NK cells (CD16) | |||||
| Mean (SD) | 285 (160) | 367 (269) | 290 (316) | 700 (692) | 360 (392) |
| Median [Min, Max] | 245 [35.0, 659] | 309 [17.0, 1060] | 173 [9.00, 1580] | 567 [11.0, 2910] | 260 [9.00, 2910] |
| Missing | 3 (10.7%) | 1 (5.0%) | 4 (5.6%) | 1 (5.0%) | 9 (6.5%) |
## Stratified by symptom
## autoimmunity diarrhea infection
## n 28 20 71
## CD3_category = CD3_low (%) 19 (70.4) 5 ( 25.0) 57 (80.3)
## CD3_CD4_category = CD3/CD4_low (%) 15 (55.6) 2 ( 10.0) 47 (66.2)
## CD3_CD8_category = CD3/CD8_low (%) 17 (65.4) 13 ( 65.0) 60 (84.5)
## CD4_CD8_ratio_category = CD4:CD8_low (%) 16 (64.0) 9 ( 52.9) 37 (55.2)
## CD19_category = CD19_low (%) 17 (65.4) 20 (100.0) 59 (88.1)
## NKcell_CD16_category = CD19_low (%) 14 (56.0) 8 ( 42.1) 41 (61.2)
## Stratified by symptom
## lymphoproliferation p test
## n 20
## CD3_category = CD3_low (%) 5 (25.0) <0.001
## CD3_CD4_category = CD3/CD4_low (%) 1 ( 5.0) <0.001
## CD3_CD8_category = CD3/CD8_low (%) 8 (40.0) 0.001
## CD4_CD8_ratio_category = CD4:CD8_low (%) 8 (47.1) 0.736
## CD19_category = CD19_low (%) 11 (57.9) 0.001
## NKcell_CD16_category = CD19_low (%) 7 (36.8) 0.190| autoimmunity (N=28) |
diarrhea (N=20) |
infection (N=71) |
lymphoproliferation (N=20) |
Total (N=139) |
|
|---|---|---|---|---|---|
| CD3_category | |||||
| CD3_high | 8 (28.6%) | 15 (75.0%) | 14 (19.7%) | 15 (75.0%) | 52 (37.4%) |
| CD3_low | 19 (67.9%) | 5 (25.0%) | 57 (80.3%) | 5 (25.0%) | 86 (61.9%) |
| Missing | 1 (3.6%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (0.7%) |
| CD3_CD4_category | |||||
| CD3/CD4_high | 12 (42.9%) | 18 (90.0%) | 24 (33.8%) | 19 (95.0%) | 73 (52.5%) |
| CD3/CD4_low | 15 (53.6%) | 2 (10.0%) | 47 (66.2%) | 1 (5.0%) | 65 (46.8%) |
| Missing | 1 (3.6%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (0.7%) |
| CD3_CD8_category | |||||
| CD3/CD8_high | 9 (32.1%) | 7 (35.0%) | 11 (15.5%) | 12 (60.0%) | 39 (28.1%) |
| CD3/CD8_low | 17 (60.7%) | 13 (65.0%) | 60 (84.5%) | 8 (40.0%) | 98 (70.5%) |
| Missing | 2 (7.1%) | 0 (0%) | 0 (0%) | 0 (0%) | 2 (1.4%) |
| CD4_CD8_ratio_category | |||||
| CD4:CD8_high | 9 (32.1%) | 8 (40.0%) | 30 (42.3%) | 9 (45.0%) | 56 (40.3%) |
| CD4:CD8_low | 16 (57.1%) | 9 (45.0%) | 37 (52.1%) | 8 (40.0%) | 70 (50.4%) |
| Missing | 3 (10.7%) | 3 (15.0%) | 4 (5.6%) | 3 (15.0%) | 13 (9.4%) |
| CD19_category | |||||
| CD19_high | 9 (32.1%) | 0 (0%) | 8 (11.3%) | 8 (40.0%) | 25 (18.0%) |
| CD19_low | 17 (60.7%) | 20 (100%) | 59 (83.1%) | 11 (55.0%) | 107 (77.0%) |
| Missing | 2 (7.1%) | 0 (0%) | 4 (5.6%) | 1 (5.0%) | 7 (5.0%) |
| NKcell_CD16_category | |||||
| CD19_high | 11 (39.3%) | 11 (55.0%) | 26 (36.6%) | 12 (60.0%) | 60 (43.2%) |
| CD19_low | 14 (50.0%) | 8 (40.0%) | 41 (57.7%) | 7 (35.0%) | 70 (50.4%) |
| Missing | 3 (10.7%) | 1 (5.0%) | 4 (5.6%) | 1 (5.0%) | 9 (6.5%) |
## Stratified by symptom
## autoimmunity diarrhea infection
## n 28 20 71
## CD3_CD4_category = CD3/CD4_low (%) 15 (55.6) 2 (10.0) 47 (66.2)
## Stratified by symptom
## lymphoproliferation p test
## n 20
## CD3_CD4_category = CD3/CD4_low (%) 1 (5.0) <0.001| autoimmunity (N=28) |
diarrhea (N=20) |
infection (N=71) |
lymphoproliferation (N=20) |
Total (N=139) |
|
|---|---|---|---|---|---|
| CD3_CD4_category | |||||
| CD3/CD4_high | 12 (42.9%) | 18 (90.0%) | 24 (33.8%) | 19 (95.0%) | 73 (52.5%) |
| CD3/CD4_low | 15 (53.6%) | 2 (10.0%) | 47 (66.2%) | 1 (5.0%) | 65 (46.8%) |
| Missing | 1 (3.6%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (0.7%) |
## Stratified by symptom
## autoimmunity diarrhea infection
## n 28 20 71
## CD19_category = CD19_low (%) 17 (65.4) 20 (100.0) 59 (88.1)
## Stratified by symptom
## lymphoproliferation p test
## n 20
## CD19_category = CD19_low (%) 11 (57.9) 0.001| autoimmunity (N=28) |
diarrhea (N=20) |
infection (N=71) |
lymphoproliferation (N=20) |
Total (N=139) |
|
|---|---|---|---|---|---|
| CD19_category | |||||
| CD19_high | 9 (32.1%) | 0 (0%) | 8 (11.3%) | 8 (40.0%) | 25 (18.0%) |
| CD19_low | 17 (60.7%) | 20 (100%) | 59 (83.1%) | 11 (55.0%) | 107 (77.0%) |
| Missing | 2 (7.1%) | 0 (0%) | 4 (5.6%) | 1 (5.0%) | 7 (5.0%) |
##
## Call:
## glm(formula = CD3_CD4_category_dicho ~ symptom + age, family = binomial,
## data = data)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.4344 -0.9165 0.3179 1.2587 1.5300
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.186784 0.417382 -0.448 0.65450
## symptomdiarrhea 2.400668 0.844132 2.844 0.00446 **
## symptominfection -0.461539 0.464821 -0.993 0.32074
## symptomlymphoproliferation 3.148159 1.099693 2.863 0.00420 **
## age -0.003205 0.013783 -0.233 0.81610
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 190.84 on 137 degrees of freedom
## Residual deviance: 148.83 on 133 degrees of freedom
## (1 observation deleted due to missingness)
## AIC: 158.83
##
## Number of Fisher Scoring iterations: 5##
## Call:
## glm(formula = CD3_CD4_category_dicho ~ symptom + age + CD19_category,
## family = binomial, data = data)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -2.2925 -0.8637 0.2247 0.9626 1.5324
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 0.460507 0.564616 0.816 0.4147
## symptomdiarrhea 2.860328 0.882979 3.239 0.0012 **
## symptominfection -0.135869 0.512269 -0.265 0.7908
## symptomlymphoproliferation 3.204570 1.119410 2.863 0.0042 **
## age 0.001051 0.014653 0.072 0.9428
## CD19_categoryCD19_low -1.128994 0.561069 -2.012 0.0442 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 180.99 on 130 degrees of freedom
## Residual deviance: 137.14 on 125 degrees of freedom
## (8 observations deleted due to missingness)
## AIC: 149.14
##
## Number of Fisher Scoring iterations: 5##
## Call:
## glm(formula = CD19_category_dicho ~ symptom + age, family = binomial,
## data = data)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.07460 -0.52759 -0.51423 -0.00013 2.03777
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -0.49054 0.45529 -1.077 0.2813
## symptomdiarrhea -18.00477 1457.35179 -0.012 0.9901
## symptominfection -1.40895 0.56452 -2.496 0.0126 *
## symptomlymphoproliferation 0.24854 0.62833 0.396 0.6924
## age -0.01426 0.02013 -0.708 0.4788
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 128.13 on 131 degrees of freedom
## Residual deviance: 107.85 on 127 degrees of freedom
## (7 observations deleted due to missingness)
## AIC: 117.85
##
## Number of Fisher Scoring iterations: 17##
## Call:
## glm(formula = CD19_category_dicho ~ symptom + age + CD3_category +
## CD3_CD4_category, family = binomial, data = data)
##
## Deviance Residuals:
## Min 1Q Median 3Q Max
## -1.24331 -0.66707 -0.33930 -0.00015 2.40271
##
## Coefficients:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) 8.717e-01 6.440e-01 1.354 0.17588
## symptomdiarrhea -1.909e+01 1.400e+03 -0.014 0.98912
## symptominfection -1.460e+00 6.099e-01 -2.394 0.01667 *
## symptomlymphoproliferation -8.196e-01 7.624e-01 -1.075 0.28237
## age -1.469e-03 1.946e-02 -0.075 0.93984
## CD3_categoryCD3_low -1.527e+00 5.893e-01 -2.591 0.00956 **
## CD3_CD4_categoryCD3/CD4_low -7.093e-01 6.148e-01 -1.154 0.24862
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## (Dispersion parameter for binomial family taken to be 1)
##
## Null deviance: 127.709 on 130 degrees of freedom
## Residual deviance: 95.938 on 124 degrees of freedom
## (8 observations deleted due to missingness)
## AIC: 109.94
##
## Number of Fisher Scoring iterations: 17