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library(knitr)
library(readr)
library(dplyr)
## 
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
library(tidyr)
library(broom)
library(ggplot2)
library(ggpubr)
## Loading required package: magrittr
## 
## Attaching package: 'magrittr'
## The following object is masked from 'package:tidyr':
## 
##     extract

comparing residuals of subcortical volume (controlling for age, sex, ICV, and education level)among different HC groups

Region statistic p.value parameter method
Laccumb_vol 1.3376520 0.7202122 3 Kruskal-Wallis rank sum test
Lamyg_vol 4.3622373 0.2249125 3 Kruskal-Wallis rank sum test
Lcaud_vol 1.8834962 0.5969359 3 Kruskal-Wallis rank sum test
Lhippo_vol 3.2192710 0.3590376 3 Kruskal-Wallis rank sum test
Lput_vol 1.6390466 0.6505690 3 Kruskal-Wallis rank sum test
Lthal_vol 2.0494215 0.5622127 3 Kruskal-Wallis rank sum test
Raccumb_vol 0.6138843 0.8932467 3 Kruskal-Wallis rank sum test
Ramyg_vol 1.4802937 0.6868259 3 Kruskal-Wallis rank sum test
Rcaud_vol 4.7940230 0.1875162 3 Kruskal-Wallis rank sum test
Rhippo_vol 2.0405579 0.5640316 3 Kruskal-Wallis rank sum test
Rput_vol 2.8194687 0.4203050 3 Kruskal-Wallis rank sum test
Rthal_vol 1.8784578 0.5980122 3 Kruskal-Wallis rank sum test

comparing residuals of cortical thickness (controlling for age, sex, and education level) among different HC groups

Region statistic p.value parameter method
L_caudalanteriorcingulate_thickavg 2.5539464 0.4656206 3 Kruskal-Wallis rank sum test
L_caudalmiddlefrontal_thickavg 1.1078284 0.7751846 3 Kruskal-Wallis rank sum test
L_entorhinal_thickavg 1.4718090 0.6887919 3 Kruskal-Wallis rank sum test
L_inferiortemporal_thickavg 1.5251065 0.6764880 3 Kruskal-Wallis rank sum test
L_lateralorbitofrontal_thickavg 0.8817518 0.8298291 3 Kruskal-Wallis rank sum test
L_medialorbitofrontal_thickavg 0.8369693 0.8406056 3 Kruskal-Wallis rank sum test
L_parahippocampal_thickavg 5.5257926 0.1371040 3 Kruskal-Wallis rank sum test
L_parsopercularis_thickavg 4.4137067 0.2201178 3 Kruskal-Wallis rank sum test
L_parsorbitalis_thickavg 1.1317674 0.7694114 3 Kruskal-Wallis rank sum test
L_parstriangularis_thickavg 2.0860143 0.5547473 3 Kruskal-Wallis rank sum test
L_posteriorcingulate_thickavg 0.5228730 0.9138383 3 Kruskal-Wallis rank sum test
L_precuneus_thickavg 0.7992748 0.8496405 3 Kruskal-Wallis rank sum test
L_rostralanteriorcingulate_thickavg 0.4374528 0.9324015 3 Kruskal-Wallis rank sum test
L_rostralmiddlefrontal_thickavg 2.2513148 0.5219118 3 Kruskal-Wallis rank sum test
L_superiorfrontal_thickavg 3.5026306 0.3204211 3 Kruskal-Wallis rank sum test
L_superiorparietal_thickavg 0.2134037 0.9753970 3 Kruskal-Wallis rank sum test
L_superiortemporal_thickavg 0.4477815 0.9302043 3 Kruskal-Wallis rank sum test
R_caudalanteriorcingulate_thickavg 0.6936774 0.8746901 3 Kruskal-Wallis rank sum test
R_caudalmiddlefrontal_thickavg 1.3775879 0.7107966 3 Kruskal-Wallis rank sum test
R_entorhinal_thickavg 1.4873025 0.6852040 3 Kruskal-Wallis rank sum test
R_inferiortemporal_thickavg 2.5469392 0.4668678 3 Kruskal-Wallis rank sum test
R_lateralorbitofrontal_thickavg 0.9725916 0.8078836 3 Kruskal-Wallis rank sum test
R_medialorbitofrontal_thickavg 1.3345885 0.7209365 3 Kruskal-Wallis rank sum test
R_parahippocampal_thickavg 3.8836592 0.2743040 3 Kruskal-Wallis rank sum test
R_parsopercularis_thickavg 2.4716683 0.4804330 3 Kruskal-Wallis rank sum test
R_parsorbitalis_thickavg 2.0945328 0.5530196 3 Kruskal-Wallis rank sum test
R_parstriangularis_thickavg 1.1188206 0.7725328 3 Kruskal-Wallis rank sum test
R_posteriorcingulate_thickavg 1.8251458 0.6094783 3 Kruskal-Wallis rank sum test
R_precuneus_thickavg 0.5737108 0.9024234 3 Kruskal-Wallis rank sum test
R_rostralanteriorcingulate_thickavg 0.1579545 0.9840731 3 Kruskal-Wallis rank sum test
R_rostralmiddlefrontal_thickavg 0.5619366 0.9050881 3 Kruskal-Wallis rank sum test
R_superiorfrontal_thickavg 0.8723533 0.8320939 3 Kruskal-Wallis rank sum test
R_superiorparietal_thickavg 0.4942177 0.9201599 3 Kruskal-Wallis rank sum test
R_superiortemporal_thickavg 0.5064689 0.9174679 3 Kruskal-Wallis rank sum test

comparing residuals of FA value (controlling for age, sex, and education level) among different HC groups

tract statistic p.value parameter method
CGC.L_FA 2.545620 0.4671029 3 Kruskal-Wallis rank sum test
CGC.R_FA 2.645782 0.4495199 3 Kruskal-Wallis rank sum test
CGH.L_FA 1.736672 0.6288118 3 Kruskal-Wallis rank sum test
CGH.R_FA 1.354319 0.7162766 3 Kruskal-Wallis rank sum test
FX.ST.L_FA 9.940948 0.0190748 3 Kruskal-Wallis rank sum test
FX.ST.R_FA 4.634474 0.2006046 3 Kruskal-Wallis rank sum test
GCC_FA 2.515526 0.4724918 3 Kruskal-Wallis rank sum test
SCC_FA 1.662763 0.6452440 3 Kruskal-Wallis rank sum test
SLF_FA 3.486714 0.3224893 3 Kruskal-Wallis rank sum test
SLF.L_FA 4.889986 0.1800324 3 Kruskal-Wallis rank sum test
SLF.R_FA 1.495918 0.6832128 3 Kruskal-Wallis rank sum test
UNC.L_FA 3.894771 0.2730535 3 Kruskal-Wallis rank sum test
UNC.R_FA 1.774328 0.6205373 3 Kruskal-Wallis rank sum test

post-hoc testing with adjusted p value in one region that is significantly different among groups

## Warning in wilcox.test.default(xi, xj, paired = paired, ...): cannot
## compute exact p-value with ties
## 
##  Pairwise comparisons using Wilcoxon rank sum test 
## 
## data:  FAval$FX.ST.L_FA and FAval$study 
## 
##         DTI3T PACtMD PAS-AD
## PACtMD  0.856 -      -     
## PAS-AD  0.788 0.788  -     
## rTMS-AD 0.009 0.009  0.119 
## 
## P value adjustment method: BH

comparing residuals of MD value (controlling for age, sex, and education level) among different HC groups

tract statistic p.value parameter method
CGC.L_MD 0.7297483 0.8661855 3 Kruskal-Wallis rank sum test
CGC.R_MD 1.4433214 0.6954121 3 Kruskal-Wallis rank sum test
CGH.L_MD 3.2082735 0.3606146 3 Kruskal-Wallis rank sum test
CGH.R_MD 5.9181314 0.1156620 3 Kruskal-Wallis rank sum test
FX.ST.L_MD 1.2822392 0.7333548 3 Kruskal-Wallis rank sum test
FX.ST.R_MD 2.3841718 0.4965878 3 Kruskal-Wallis rank sum test
GCC_MD 7.4220835 0.0595946 3 Kruskal-Wallis rank sum test
SCC_MD 0.5811978 0.9007229 3 Kruskal-Wallis rank sum test
SLF_MD 4.0118550 0.2601868 3 Kruskal-Wallis rank sum test
SLF.L_MD 3.9674911 0.2649960 3 Kruskal-Wallis rank sum test
SLF.R_MD 3.5501044 0.3143217 3 Kruskal-Wallis rank sum test
UNC.L_MD 0.0963962 0.9922664 3 Kruskal-Wallis rank sum test
UNC.R_MD 0.6755969 0.8789282 3 Kruskal-Wallis rank sum test