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1_merge FA, MD, RD, AD within site_v.21.11.21.R
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1_merge FA, MD, RD, AD within site_v.21.11.21.R
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library(tidyverse)
library(naniar)
library(skimr)
# Merging data of each site.
# subjectID
# covariate: 17
# FA, MD, RD, AD measure: 63
#### Make list for column name ####
list_cov <- c('Dx','Age','AgeSQ','Sex','Med','AO','Dur','Sev','Agr_Check','Clean','Sex_Rel','Hoard','Ord','Anx','CurAnx','Dep','CurDep')
list_FA <- c('ACR.FA', 'ACR.L.FA', 'ACR.R.FA', 'ALIC.FA', 'ALIC.L.FA', 'ALIC.R.FA', 'AverageFA', 'BCC.FA', 'CC.FA', 'CGC.FA', 'CGC.L.FA', 'CGC.R.FA', 'CGH.FA', 'CGH.L.FA', 'CGH.R.FA', 'CR.FA', 'CR.L.FA', 'CR.R.FA', 'CST.FA', 'CST.L.FA', 'CST.R.FA', 'EC.FA', 'EC.L.FA', 'EC.R.FA', 'FX.FA', 'FX.ST.L.FA', 'FX.ST.R.FA', 'FXST.FA', 'GCC.FA', 'IC.FA', 'IC.L.FA', 'IC.R.FA', 'IFO.FA', 'IFO.L.FA', 'IFO.R.FA', 'PCR.FA', 'PCR.L.FA', 'PCR.R.FA', 'PLIC.FA', 'PLIC.L.FA', 'PLIC.R.FA', 'PTR.FA', 'PTR.L.FA', 'PTR.R.FA', 'RLIC.FA', 'RLIC.L.FA', 'RLIC.R.FA', 'SCC.FA', 'SCR.FA', 'SCR.L.FA', 'SCR.R.FA', 'SFO.FA', 'SFO.L.FA', 'SFO.R.FA', 'SLF.FA', 'SLF.L.FA', 'SLF.R.FA', 'SS.FA', 'SS.L.FA', 'SS.R.FA', 'UNC.FA', 'UNC.L.FA', 'UNC.R.FA')
list_MD <- c('ACR.MD', 'ACR.L.MD', 'ACR.R.MD', 'ALIC.MD', 'ALIC.L.MD', 'ALIC.R.MD', 'AverageMD', 'BCC.MD', 'CC.MD', 'CGC.MD', 'CGC.L.MD', 'CGC.R.MD', 'CGH.MD', 'CGH.L.MD', 'CGH.R.MD', 'CR.MD', 'CR.L.MD', 'CR.R.MD', 'CST.MD', 'CST.L.MD', 'CST.R.MD', 'EC.MD', 'EC.L.MD', 'EC.R.MD', 'FX.MD', 'FX.ST.L.MD', 'FX.ST.R.MD', 'FXST.MD', 'GCC.MD', 'IC.MD', 'IC.L.MD', 'IC.R.MD', 'IFO.MD', 'IFO.L.MD', 'IFO.R.MD', 'PCR.MD', 'PCR.L.MD', 'PCR.R.MD', 'PLIC.MD', 'PLIC.L.MD', 'PLIC.R.MD', 'PTR.MD', 'PTR.L.MD', 'PTR.R.MD', 'RLIC.MD', 'RLIC.L.MD', 'RLIC.R.MD', 'SCC.MD', 'SCR.MD', 'SCR.L.MD', 'SCR.R.MD', 'SFO.MD', 'SFO.L.MD', 'SFO.R.MD', 'SLF.MD', 'SLF.L.MD', 'SLF.R.MD', 'SS.MD', 'SS.L.MD', 'SS.R.MD', 'UNC.MD', 'UNC.L.MD', 'UNC.R.MD')
list_RD <- c( 'ACR.RD', 'ACR.L.RD', 'ACR.R.RD', 'ALIC.RD', 'ALIC.L.RD', 'ALIC.R.RD', 'AverageRD', 'BCC.RD', 'CC.RD', 'CGC.RD', 'CGC.L.RD', 'CGC.R.RD', 'CGH.RD', 'CGH.L.RD', 'CGH.R.RD', 'CR.RD', 'CR.L.RD', 'CR.R.RD', 'CST.RD', 'CST.L.RD', 'CST.R.RD', 'EC.RD', 'EC.L.RD', 'EC.R.RD', 'FX.RD', 'FX.ST.L.RD', 'FX.ST.R.RD', 'FXST.RD', 'GCC.RD', 'IC.RD', 'IC.L.RD', 'IC.R.RD', 'IFO.RD', 'IFO.L.RD', 'IFO.R.RD', 'PCR.RD', 'PCR.L.RD', 'PCR.R.RD', 'PLIC.RD', 'PLIC.L.RD', 'PLIC.R.RD', 'PTR.RD', 'PTR.L.RD', 'PTR.R.RD', 'RLIC.RD', 'RLIC.L.RD', 'RLIC.R.RD', 'SCC.RD', 'SCR.RD', 'SCR.L.RD', 'SCR.R.RD', 'SFO.RD', 'SFO.L.RD', 'SFO.R.RD', 'SLF.RD', 'SLF.L.RD', 'SLF.R.RD', 'SS.RD', 'SS.L.RD', 'SS.R.RD', 'UNC.RD', 'UNC.L.RD', 'UNC.R.RD')
list_AD <- c( 'ACR.AD', 'ACR.L.AD', 'ACR.R.AD', 'ALIC.AD', 'ALIC.L.AD', 'ALIC.R.AD', 'AverageAD', 'BCC.AD', 'CC.AD', 'CGC.AD', 'CGC.L.AD', 'CGC.R.AD', 'CGH.AD', 'CGH.L.AD', 'CGH.R.AD', 'CR.AD', 'CR.L.AD', 'CR.R.AD', 'CST.AD', 'CST.L.AD', 'CST.R.AD', 'EC.AD', 'EC.L.AD', 'EC.R.AD', 'FX.AD', 'FX.ST.L.AD', 'FX.ST.R.AD', 'FXST.AD', 'GCC.AD', 'IC.AD', 'IC.L.AD', 'IC.R.AD', 'IFO.AD', 'IFO.L.AD', 'IFO.R.AD', 'PCR.AD', 'PCR.L.AD', 'PCR.R.AD', 'PLIC.AD', 'PLIC.L.AD', 'PLIC.R.AD', 'PTR.AD', 'PTR.L.AD', 'PTR.R.AD', 'RLIC.AD', 'RLIC.L.AD', 'RLIC.R.AD', 'SCC.AD', 'SCR.AD', 'SCR.L.AD', 'SCR.R.AD', 'SFO.AD', 'SFO.L.AD', 'SFO.R.AD', 'SLF.AD', 'SLF.L.AD', 'SLF.R.AD', 'SS.AD', 'SS.L.AD', 'SS.R.AD', 'UNC.AD', 'UNC.L.AD', 'UNC.R.AD')
# FA, MD, RD, AD: 63 variables
#### 1. Amsterdam ####
#### 1. Amsterdam - Data load####
# Number of subject
'''
79 > 72 : due to no covariate including age, sex, diagnosis
# Number of column
- combined ROI: 81
- MD: 67
- RD: 67
- AD: 67
# merged: 79*273
'''
# combined ROI
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/1.FA")
AmsterdamcombinedROItable = read.csv(file='amsterdam_combinedROItable.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# MD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/2.MD")
AmsterdamMD = read.csv(file='Amsterdam_VUMC_combinedROItable_MD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# RD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/3.RD")
AmsterdamRD = read.csv(file='Amsterdam_VUMC_combinedROItable_RD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# AD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/4.AD")
AmsterdamAD = read.csv(file='Amsterdam_VUMC_combinedROItable_AD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
AmsterdamcombinedROItable
AmsterdamMD
AmsterdamRD
AmsterdamAD
#
names(AmsterdamcombinedROItable)[1] <- 'subjectID'
#### 1. Amsterdam - variable name setting - DTI ####
# COmbined ROI
which(colnames(AmsterdamcombinedROItable) == "ACR")
ncol(AmsterdamcombinedROItable)
names(AmsterdamcombinedROItable[19:81])
length(names(AmsterdamcombinedROItable[19:81]))
AmsterdamcombinedROItable <- AmsterdamcombinedROItable[1:18] %>%
bind_cols(setNames(AmsterdamcombinedROItable[19:81], list_FA))
# MD
which(colnames(AmsterdamMD) == "ACR")
ncol(AmsterdamMD)
67-4
AmsterdamMD <- AmsterdamMD[1:4] %>%
bind_cols(setNames(AmsterdamMD[5:67], list_MD))
# RD
which(colnames(AmsterdamRD) == "ACR")
ncol(AmsterdamRD)
AmsterdamRD <- AmsterdamRD[1:4] %>%
bind_cols(setNames(AmsterdamRD[5:67], list_RD))
# AD
which(colnames(AmsterdamAD) == 'ACR')
ncol(AmsterdamAD)
AmsterdamAD <- AmsterdamAD[1:4] %>%
bind_cols(setNames(AmsterdamAD[5:67], list_AD))
#### 1. Amsterdam - Arrange####
AmsterdamcombinedROItable <- AmsterdamcombinedROItable %>%
arrange(subjectID)
AmsterdamMD <- AmsterdamMD %>%
arrange(subjectID)
AmsterdamRD <- AmsterdamRD %>%
arrange(subjectID)
AmsterdamAD <- AmsterdamAD %>%
arrange(subjectID)
#### 1. Amsterdam - Merge ####
Amsterdam_merged <- AmsterdamcombinedROItable %>%
bind_cols(AmsterdamMD %>% select(-c(subjectID, Age, Sex, Diagnosis))) %>%
bind_cols(AmsterdamRD %>% select(-c(subjectID, Age, Sex, Diagnosis))) %>%
bind_cols(AmsterdamAD %>% select(-c(subjectID, Age, Sex, Diagnosis)))
#### 2. Bangalore ####
#### 2. Bangalore - Load data ####
'''
# Number of subject
- combinedROI: 290
- the others:
# Number of column
- combined ROI: 81
- MD: 80 > 67
- RD: 80 > 67
- AD: 80 > 67
# merged : 290 * 273
'''
# combined ROI
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/1.FA")
BangalorecombinedROItable = read.csv(file='bangelore_combinedroitablefa.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# MD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/2.MD")
BangaloreMD = read.csv(file='Bangalore_combinedROItable_MD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# RD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/3.RD")
BangaloreRD = read.csv(file='Bangalore_combinedROItable_RD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# AD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/4.AD")
BangaloreAD = read.csv(file='Bangalore_combinedROItable_AD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
BangalorecombinedROItable
BangaloreMD
BangaloreRD
BangaloreAD
#### 2. Bangalore - Variable name setting - covariates ####
names(BangalorecombinedROItable)[1] <- 'subjectID'
BangalorecombinedROItable <- rename(BangalorecombinedROItable, Sex_Rel = Sex_rel)
BangalorecombinedROItable <- rename(BangalorecombinedROItable, AgeSQ = AgeSq)
#### 2. Bangalore - Variable order setting ####
BangalorecombinedROItable<- BangalorecombinedROItable %>% relocate(c(subjectID, Dx, Age, AgeSQ, Sex, Med, AO, Dur, Sev, Agr_Check, Clean, Sex_Rel, Hoard, Ord, Anx, CurAnx, Dep, CurDep))
#### 2. Bangalore - Variable name setting - DTI ####
# combined ROI
which(colnames(BangalorecombinedROItable) =="ACR.fa") # 19
ncol(BangalorecombinedROItable) # 81
BangalorecombinedROItable <- BangalorecombinedROItable[1:18] %>%
bind_cols(setNames(BangalorecombinedROItable[19:81], list_FA))
# MD
which(colnames(BangaloreMD) == "ACR.md") # 19
ncol(BangaloreMD) #81
BangaloreMD <- BangaloreMD[1:18] %>%
bind_cols(setNames(BangaloreMD[19:81], list_MD))
# RD
which(colnames(BangaloreRD) == "ACR.rd")
ncol(BangaloreRD)
BangaloreRD <- BangaloreRD[1:18] %>%
bind_cols(setNames(BangaloreRD[19:81], list_RD))
# AD
which(colnames(BangaloreAD) == 'ACR.ad')
ncol(BangaloreAD)
BangaloreAD <- BangaloreAD[1:18] %>%
bind_cols(setNames(BangaloreAD[19:81], list_AD))
#### 2. Bangalore - arrange####
BangalorecombinedROItable <- BangalorecombinedROItable %>%
arrange(subjectID)
BangaloreMD <- BangaloreMD %>%
arrange(subjectID)
BangaloreRD <- BangaloreRD %>%
arrange(subjectID)
BangaloreAD <- BangaloreAD %>%
arrange(subjectID)
#### 2. Bangalore - Merge ####
# Data merge
Bangalore_merged <- BangalorecombinedROItable %>%
bind_cols(BangaloreMD %>% select(-c(subjectID, Age, Sex, Dx, AgeSq, Med, AO, Dur, Sev, Agr_Check, Clean, Sex_rel, Hoard, Ord, Anx, Dep, CurAnx, CurDep))) %>%
bind_cols(BangaloreRD %>% select(-c(subjectID, Age, Sex, Dx, AgeSq, Med, AO, Dur, Sev, Agr_Check, Clean, Sex_rel, Hoard, Ord, Anx, Dep, CurAnx, CurDep))) %>%
bind_cols(BangaloreAD %>% select(-c(subjectID, Age, Sex, Diagnosis, AgeSq, Med, AO, Dur, Sev, Agr_Check, Clean, Sex_rel, Hoard, Ord, Anx, Dep, CurAnx, CurDep)))
#### 3. Capetown ####
#### 3. Capetown - Load dataset ####
# combined ROI
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/1.FA")
CapetowncombinedROItable = read.csv(file='capetown_combinedROItable.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# MD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/2.MD")
CapetownMD = read.csv(file='CapeTown_combinedROItable_MD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# RD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/3.RD")
CapetownRD = read.csv(file='CapeTown_combinedROItable_RD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# AD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/4.AD")
CapetownAD = read.csv(file='CapeTown_combinedROItable_AD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
CapetowncombinedROItable
CapetownMD
CapetownRD
CapetownAD
#### 3. Capetown - Variable setting -covariate ####
names(CapetowncombinedROItable)[1] <- 'subjectID'
CapetowncombinedROItable <- rename(CapetowncombinedROItable, AgeSQ = agesq)
#### 3. Capetown - Variable name setting - DTI ####
# combined ROI
which(colnames(CapetowncombinedROItable) == "ACR")
ncol(CapetowncombinedROItable)
CapetowncombinedROItable<- CapetowncombinedROItable[1:18] %>%
bind_cols(setNames(CapetowncombinedROItable[19:81], list_FA))
# MD
which(colnames(CapetownMD) == "ACR")
ncol(CapetownMD)
CapetownMD <- CapetownMD[1:4] %>%
bind_cols(setNames(CapetownMD[5:67], list_MD))
# RD
which(colnames(CapetownRD) == "ACR")
ncol(CapetownRD)
CapetownRD <- CapetownRD[1:4] %>%
bind_cols(setNames(CapetownRD[5:67], list_RD))
# AD
which(colnames(CapetownAD) == "ACR")
ncol(CapetownAD)
CapetownAD <- CapetownAD[1:4] %>%
bind_cols(setNames(CapetownAD[5:67], list_AD))
#### 3. Capetown - Arrange ####
CapetowncombinedROItable <- CapetowncombinedROItable %>%
arrange(subjectID)
CapetownMD <- CapetownMD %>%
arrange(subjectID)
CapetownRD <- CapetownRD %>%
arrange(subjectID)
CapetownAD <- CapetownAD %>%
arrange(subjectID)
#### 3. Capetown - Merge ####
Capetown_merged <- CapetowncombinedROItable %>%
bind_cols(CapetownMD %>% select(-c(subjectID, Age, Sex, Diagnosis))) %>%
bind_cols(CapetownRD %>% select(-c(subjectID, Age, Sex, Diagnosis))) %>%
bind_cols(CapetownAD %>% select(-c(subjectID, Age, Sex, Diagnosis)))
#### 4. Kyoto ####
# without Dx in combined ROI
# without AgeSQ in combined ROI
#### 4. Kyoto - Load dataset ####
# combined ROI
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/1.FA")
KyotocombinedROItable = read.csv(file='kyotocombinedROItable.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# MD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/2.MD")
KyotoMD = read.csv(file='Kyoto_combinedROItable_MD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# RD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/3.RD")
KyotoRD = read.csv(file='Kyoto_combinedROItable_RD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# AD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/4.AD")
KyotoAD = read.csv(file='Kyoto_combinedROItable_AD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
KyotocombinedROItable
KyotoMD
KyotoRD
KyotoAD
#### 4. Kyoto - set variable name ####
names(KyotocombinedROItable)[1] <- 'subjectID'
KyotocombinedROItable$AgeSQ <- NA # make AgeSQ variable
KyotocombinedROItable <- rename(KyotocombinedROItable, Sex_Rel = Sex_ReI)
KyotocombinedROItable <- KyotocombinedROItable %>%
inner_join(KyotoMD %>% select(subjectID, Dx), by = 'subjectID') # Make Dx in combined ROI file
#### 4. Kyoto - set variable order - covariate####
# remove redundant variable: Sex.1
KyotocombinedROItable <- KyotocombinedROItable %>%
select(-Sex.1)
# reordering
KyotocombinedROItable<- KyotocombinedROItable %>% relocate(c(subjectID,
Dx,
Age,
AgeSQ,
Sex,
Med,
AO,
Dur,
Sev,
Agr_Check,
Clean,
Sex_Rel,
Hoard,
Ord,
Anx,
CurAnx,
Dep,
CurDep))
#### 4. Kyoto - set variable order - DTI ####
# combined ROI
which(colnames(KyotocombinedROItable) == "ACR")
ncol(KyotocombinedROItable)
KyotocombinedROItable<- KyotocombinedROItable[1:18] %>%
bind_cols(setNames(KyotocombinedROItable[19:81], list_FA))
# MD
which(colnames(KyotoMD) == "ACR")
ncol(KyotoMD)
KyotoMD <- KyotoMD[1:4] %>%
bind_cols(setNames(KyotoMD[5:67], list_MD))
# RD
which(colnames(KyotoRD) == "ACR")
ncol(KyotoRD)
KyotoRD <- KyotoRD[1:4] %>%
bind_cols(setNames(KyotoRD[5:67], list_RD))
# AD
which(colnames(KyotoAD) == "ACR")
ncol(KyotoAD)
KyotoAD <- KyotoAD[1:4] %>%
bind_cols(setNames(KyotoAD[5:67], list_AD))
#### 4. Kyoto - Arrange ####
# arrange
KyotocombinedROItable <- KyotocombinedROItable %>%
arrange(subjectID)
KyotoMD <- KyotoMD %>%
arrange(subjectID)
KyotoRD <- KyotoRD %>%
arrange(subjectID)
KyotoAD <- KyotoAD %>%
arrange(subjectID)
#### 4. Kyoto - Merge ####
Kyoto_merged <- KyotocombinedROItable %>%
bind_cols(KyotoMD %>% select(-c(subjectID, Age, Sex, Dx))) %>%
bind_cols(KyotoRD %>% select(-c(subjectID, Age, Sex, Dx))) %>%
bind_cols(KyotoAD %>% select(-c(subjectID, Age, Sex, Dx)))
Kyoto_merged
#### 5. Milan ####
#### 5. Milan - Data load ####
# combined ROI
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/1.FA")
MilancombinedROItable = read.csv(file='milan_combinedROItable.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# MD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/2.MD")
MilanMD = read.csv(file='Milan_combinedROItable_MD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# RD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/3.RD")
MilanRD = read.csv(file='Milan_combinedROItable_RD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# AD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/4.AD")
MilanAD = read.csv(file='Milan_combinedROItable_AD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
MilancombinedROItable
MilanMD
MilanRD
MilanAD
#### 5. Milan - set variable name - covariate ####
ncol(MilancombinedROItable)
MilancombinedROItable <- setNames(MilancombinedROItable[1], 'subjectID') %>%
bind_cols(MilancombinedROItable[2:80])
MilancombinedROItable$AgeSQ <- NA
MilanAD <- rename(MilanAD, Dx = Diagnosis)
#### 5. Milan - reorder variable ####
MilancombinedROItable<- MilancombinedROItable %>% relocate(c(subjectID,
Dx,
Age,
AgeSQ,
Sex,
Med,
AO,
Dur,
Sev,
Agr_Check,
Clean,
Sex_Rel,
Hoard,
Ord,
Anx,
CurAnx,
Dep,
CurDep))
#### 5. Milan - set variable name - DTI ####
which(colnames(MilancombinedROItable) == "ACR")
MilancombinedROItable <- MilancombinedROItable[1:18] %>%
bind_cols(setNames(MilancombinedROItable[19:81], list_FA))
# MD
which(colnames(MilanMD) == "ACR")
ncol(MilanMD)
MilanMD <- MilanMD[1:4] %>%
bind_cols(setNames(MilanMD[5:67], list_MD))
# RD
which(colnames(MilanRD) == "ACR")
ncol(MilanRD)
MilanRD <- MilanRD[1:4] %>%
bind_cols(setNames(MilanRD[5:67], list_RD))
# AD
which(colnames(MilanAD) == "ACR")
ncol(MilanAD)
MilanAD <- MilanAD[1:4] %>%
bind_cols(setNames(MilanAD[5:67], list_AD))
#### 5. Milan - Arrange ####
# arrange
MilancombinedROItable <- MilancombinedROItable %>%
arrange(subjectID)
MilanMD <- MilanMD %>%
arrange(subjectID)
MilanRD <- MilanRD %>%
arrange(subjectID)
MilanAD <- MilanAD %>%
arrange(subjectID)
#### 5. Milan - Merge ####
Milan_merged <- MilancombinedROItable %>%
bind_cols(MilanMD %>% select(-c(subjectID, Age, Sex, Dx))) %>%
bind_cols(MilanRD %>% select(-c(subjectID, Age, Sex, Dx))) %>%
bind_cols(MilanAD %>% select(-c(subjectID, Age, Sex, Dx)))
Milan_merged
#### 6. Mountsinai ####
#### 6. Mountsinai - Load dataset####
# combined ROI
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/1.FA")
MountsinaicombinedROItable = read.csv(file='mountsinai_combinedROItable.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# MD
setwd("..ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/2.MD")
MountsinaiMD = read.csv(file='MountSinai_combinedROItable_MD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# RD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/3.RD")
MountsinaiRD = read.csv(file='MountSinai_combinedROItable_RD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# AD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/4.AD")
MountsinaiAD = read.csv(file='MountSinai_combinedROItable_AD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
MountsinaicombinedROItable
MountsinaiMD
MountsinaiRD
MountsinaiAD
#### 6. Mountsinai - set variable name (covariate) ####
names(MountsinaicombinedROItable)[1] <- 'subjectID'
MountsinaiAD <- rename(MountsinaiAD, Dx = Diagnosis)
#### 6. Mountsinai - set variable name(DTI) ####
which(colnames(MountsinaicombinedROItable) == "ACR")
ncol(MountsinaicombinedROItable)
MountsinaicombinedROItable <- MountsinaicombinedROItable[1:18] %>%
bind_cols(setNames(MountsinaicombinedROItable[19:81], list_FA))
# MD
which(colnames(MountsinaiMD) == "ACR")
ncol(MountsinaiMD)
MountsinaiMD <- MountsinaiMD[1:4] %>%
bind_cols(setNames(MountsinaiMD[5:67], list_MD))
# RD
which(colnames(MountsinaiRD) == "ACR")
ncol(MountsinaiRD)
MountsinaiRD <- MountsinaiRD[1:4] %>%
bind_cols(setNames(MountsinaiRD[5:67], list_RD))
# AD
which(colnames(MountsinaiAD) == "ACR")
ncol(MountsinaiAD)
MountsinaiAD <- MountsinaiAD[1:4] %>%
bind_cols(setNames(MountsinaiAD[5:67], list_AD))
#### 6. Mountsinai - Arrange ####
MountsinaicombinedROItable <- MountsinaicombinedROItable %>%
arrange(subjectID)
MountsinaiMD <- MountsinaiMD %>%
arrange(subjectID)
MountsinaiRD <- MountsinaiRD %>%
arrange(subjectID)
MountsinaiAD <- MountsinaiAD %>%
arrange(subjectID)
#### 6. Mountsinai - merge ####
Mountsinai_merged <- MountsinaicombinedROItable %>%
bind_cols(MountsinaiMD %>% select(-c(subjectID, Age, Sex, Dx))) %>%
bind_cols(MountsinaiRD %>% select(-c(subjectID, Age, Sex, Dx))) %>%
bind_cols(MountsinaiAD %>% select(-c(subjectID, Age, Sex, Dx)))
#### 7. Munich ####
#### 7. Munich - Data load####
# combined ROI
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/1.FA")
MunichcombinedROItable = read.csv(file='munich_combinedROItable.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# MD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/2.MD")
MunichMD = read.csv(file='Munich_combinedROItable_MD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# RD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/3.RD")
MunichRD = read.csv(file='Munich_combinedROItable_RD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# AD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/4.AD")
MunichAD = read.csv(file='Munich_combinedROItable_AD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
MunichcombinedROItable
MunichMD
MunichRD
MunichAD
#### 7. Munich - Set variable name - covariate ####
names(MunichcombinedROItable)[1] <- 'subjectID'
MunichcombinedROItable$AgeSQ <- NA # make AgeSQ
MunichcombinedROItable <- rename(MunichcombinedROItable, Dx = dx)
MunichcombinedROItable <- rename(MunichcombinedROItable, Agr_Check = Agr_check)
MunichAD <- rename(MunichAD, Dx = Diagnosis)
#### 7. Munich - Reorder variable - covariate ####
MunichcombinedROItable<- MunichcombinedROItable %>% relocate(c(subjectID,
Dx,
Age,
AgeSQ,
Sex,
Med,
AO,
Dur,
Sev,
Agr_Check,
Clean,
Sex_Rel,
Hoard,
Ord,
Anx,
CurAnx,
Dep,
CurDep))
#### 7. Munich - set variable name - DTI ####
which(colnames(MunichcombinedROItable) == "ACR")
ncol(MunichcombinedROItable)
MunichcombinedROItable <- MunichcombinedROItable[1:18] %>%
bind_cols(setNames(MunichcombinedROItable[19:81], list_FA))
# MD
which(colnames(MunichMD) == "ACR")
ncol(MunichMD)
MunichMD <- MunichMD[1:3] %>%
bind_cols(setNames(MunichMD[4:66], list_MD))
# RD
which(colnames(MunichRD) == "ACR")
ncol(MunichRD)
MunichRD <- MunichRD[1:3] %>%
bind_cols(setNames(MunichRD[4:66], list_RD))
# AD
which(colnames(MunichAD) == "ACR")
ncol(MunichAD)
MunichAD <- MunichAD[1:4] %>%
bind_cols(setNames(MunichAD[5:67], list_AD))
#### 7. Munich - Arrange####
# arrange
MunichcombinedROItable <- MunichcombinedROItable %>%
arrange(subjectID)
MunichMD <- MunichMD %>%
arrange(subjectID)
MunichRD <- MunichRD %>%
arrange(subjectID)
MunichAD <- MunichAD %>%
arrange(subjectID)
#### 7. Munich - Merge ####
Munich_merged <- MunichcombinedROItable %>%
bind_cols(MunichMD %>% select(-c(subjectID, Age, Sex))) %>%
bind_cols(MunichRD %>% select(-c(subjectID, Age, Sex))) %>%
bind_cols(MunichAD %>% select(-c(subjectID, Age, Sex, Dx)))
Munich_merged
#### 8. Rome ####
#### 8. Rome- Load Data####
# combined ROI
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/1.FA")
RomecombinedROItable = read.csv(file='rome_combinedROItable.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# MD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/2.MD")
RomeMD = read.csv(file='Rome_combinedROItable_MD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# RD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/3.RD")
RomeRD = read.csv(file='Rome_combinedROItable_RD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# AD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/4.AD")
RomeAD = read.csv(file='Rome_combinedROItable_AD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
RomecombinedROItable
RomeMD
RomeRD
RomeAD
#### 8. Rome- Set variable name (covariate) ####
RomecombinedROItable <- setNames(RomecombinedROItable[1], 'subjectID') %>%
bind_cols(RomecombinedROItable[2:81])
#### 8. Rome- Set variable name (DTI) ####
# combined ROI
which(colnames(RomecombinedROItable) == "ACR")
ncol(RomecombinedROItable)
RomecombinedROItable <- RomecombinedROItable[1:18] %>%
bind_cols(setNames(RomecombinedROItable[19:81], list_FA))
# MD
which(colnames(RomeMD) == "ACR")
ncol(RomeMD)
RomeMD <- RomeMD[1:4] %>%
bind_cols(setNames(RomeMD[5:67], list_MD))
# RD
which(colnames(RomeRD) == "ACR")
ncol(RomeRD)
RomeRD <- RomeRD[1:4] %>%
bind_cols(setNames(RomeRD[5:67], list_RD))
# AD
which(colnames(RomeAD) == "ACR")
ncol(RomeAD)
RomeAD <- RomeAD[1:4] %>%
bind_cols(setNames(RomeAD[5:67], list_AD))
#### 8. Rome - Arrange####
RomecombinedROItable <- RomecombinedROItable %>%
arrange(subjectID)
RomeMD <- RomeMD %>%
arrange(subjectID)
RomeRD <- RomeRD %>%
arrange(subjectID)
RomeAD <- RomeAD %>%
arrange(subjectID)
#### 8. Rome- Merge####
Rome_merged <- RomecombinedROItable %>%
bind_cols(RomeMD %>% select(-c(subjectID, Age, Sex, Diagnosis))) %>%
bind_cols(RomeRD %>% select(-c(subjectID, Age, Sex, Diagnosis))) %>%
bind_cols(RomeAD %>% select(-c(subjectID, Age, Sex, Diagnosis)))
Rome_merged
#### 9. Saopaulo ####
#### 9. Saopaulo - Load dataset ####
# combined ROI
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/1.FA")
SaopaulocombinedROItable = read.csv(file='saopaulo_combinedROItable_Cha.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# MD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/2.MD")
SaopauloMD = read.csv(file='saopaolo_combinedroitable_md.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# RD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/3.RD")
SaopauloRD = read.csv(file='saopaolo_combinedroitable_rd.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# AD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/4.AD")
SaopauloAD = read.csv(file='saopaolo_combinedroitable_ad.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
SaopaulocombinedROItable
SaopauloMD
SaopauloRD
SaopauloAD
#### 9. Saopaulo - set variable name (covariate) ####
names(SaopaulocombinedROItable)[1] <- 'subjectID'
SaopaulocombinedROItable$AgeSQ <- NA
#### 9. Saopaulo - Reorder ####
SaopaulocombinedROItable<- SaopaulocombinedROItable %>% relocate(c(subjectID,
Dx,
Age,
AgeSQ,
Sex,
Med,
AO,
Dur,
Sev,
Agr_Check,
Clean,
Sex_Rel,
Hoard,
Ord,
Anx,
CurAnx,
Dep,
CurDep))
#### 9. Saopaulo -Set variable name (DTI) ####
which(colnames(SaopaulocombinedROItable) == "ACR")
ncol(SaopaulocombinedROItable)
SaopaulocombinedROItable <- SaopaulocombinedROItable[1:18] %>%
bind_cols(setNames(SaopaulocombinedROItable[19:81], list_FA))
# MD
which(colnames(SaopauloMD) == "ACR")
ncol(SaopauloMD)
SaopauloMD <- SaopauloMD[1:4] %>%
bind_cols(setNames(SaopauloMD[5:67], list_MD))
# RD
which(colnames(SaopauloRD) == "ACR")
ncol(SaopauloRD)
SaopauloRD <- SaopauloRD[1:4] %>%
bind_cols(setNames(SaopauloRD[5:67], list_RD))
# AD
which(colnames(SaopauloAD) == "ACR")
ncol(SaopauloAD)
SaopauloAD <- SaopauloAD[1:4] %>%
bind_cols(setNames(SaopauloAD[5:67], list_AD))
#### 9. Saopaulo - Arrange ####
# arrange
SaopaulocombinedROItable <- SaopaulocombinedROItable %>%
arrange(subjectID)
SaopauloMD <- SaopauloMD %>%
arrange(subjectID)
SaopauloRD <- SaopauloRD %>%
arrange(subjectID)
SaopauloAD <- SaopauloAD %>%
arrange(subjectID)
#### 9. Saopaulo - merge ####
# Data merge
Saopaulo_merged <- SaopaulocombinedROItable %>%
bind_cols(SaopauloMD %>% select(-c(subjectID, Age, Sex, Diagnosis))) %>%
bind_cols(SaopauloRD %>% select(-c(subjectID, Age, Sex, Diagnosis))) %>%
bind_cols(SaopauloAD %>% select(-c(subjectID, Age, Sex, Diagnosis)))
Saopaulo_merged
#### 10. Shanghai ####
#### 10. Shanghai - Load data####
# combined ROI
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/1.FA")
ShanghaicombinedROItable = read.csv(file='shangai_combinedROItable_updated.v.21.11.13.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# MD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/2.MD")
ShanghaiMD = read.csv(file='Shangai_combinedROItable_MD_updated.v.21.11.13.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# RD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/3.RD")
ShanghaiRD = read.csv(file='Shangai_combinedROItable_RD_updated.v.21.11.13.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# AD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/4.AD")
ShanghaiAD = read.csv(file='Shangai_combinedROItable_AD_updated.v.21.11.13.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
ShanghaicombinedROItable
ShanghaiMD
ShanghaiRD
ShanghaiAD
#### 10. Shanghai - Set variable name (Covariate) ####
#### 10. Shanghai - Set variable name (DTI) ####
#### 5. Shanghai - set variable name - DTI ####
which(colnames(ShanghaicombinedROItable) == "ACR")
ncol(ShanghaicombinedROItable)
ShanghaicombinedROItable <- ShanghaicombinedROItable[1:18] %>%
bind_cols(setNames(ShanghaicombinedROItable[19:81], list_FA))
# MD
which(colnames(ShanghaiMD) == "ACR")
ncol(ShanghaiMD)
ShanghaiMD <- ShanghaiMD[1:3] %>%
bind_cols(setNames(ShanghaiMD[4:66], list_MD))
# RD
which(colnames(ShanghaiRD) == "ACR")
ncol(ShanghaiRD)
ShanghaiRD <- ShanghaiRD[1:3] %>%
bind_cols(setNames(ShanghaiRD[4:66], list_RD))
# AD
which(colnames(ShanghaiAD) == "ACR")
ncol(ShanghaiAD)
ShanghaiAD <- ShanghaiAD[1:3] %>%
bind_cols(setNames(ShanghaiAD[4:66], list_AD))
#### 10. Shanghai - Arrange####
ShanghaicombinedROItable <- ShanghaicombinedROItable %>%
arrange(subjectID)
ShanghaiMD <- ShanghaiMD %>%
arrange(subjectID)
ShanghaiRD <- ShanghaiRD %>%
arrange(subjectID)
ShanghaiAD <- ShanghaiAD %>%
arrange(subjectID)
#### 10. Shanghai - Merge####
Shanghai_merged <- ShanghaicombinedROItable %>%
bind_cols(ShanghaiMD %>% select(-c(subjectID, Age, Sex))) %>%
bind_cols(ShanghaiRD %>% select(-c(subjectID, Age, Sex))) %>%
bind_cols(ShanghaiAD %>% select(-c(subjectID, Age, Sex)))
Shanghai_merged
#### 11. Seoul####
#### 11. Seoul - Load data####
# combined ROI
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/1.FA")
SeoulcombinedROItable = read.csv(file='seoul_updated_combinedROItable.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# MD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/2.MD")
SeoulMD = read.csv(file='Seoul_updated_combinedROItable_MD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# RD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/3.RD")
SeoulRD = read.csv(file='Seoul_updated_combinedROItable_RD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
# AD
setwd("../ENIGMA-OCD/0.Data/0_Raw_data/Data_Dti/4.AD")
SeoulAD = read.csv(file='Seoul_updated_combinedROItable_AD.csv', header = T, sep = ",", na.strings = c("NA", "")) %>% as_tibble()
SeoulcombinedROItable
SeoulMD
SeoulRD
SeoulAD
#### 11. Seoul - set variable name (covariate)####
names(SeoulcombinedROItable)[1] <- 'subjectID'
#### 11. Seoul - Reorder ####
#### 11. Seoul - Set variable name (DTI) ####
#### 5. Seoul - set variable name - DTI ####
which(colnames(SeoulcombinedROItable) == "ACR.fa")
ncol(SeoulcombinedROItable)
SeoulcombinedROItable <- SeoulcombinedROItable[1:18] %>%
bind_cols(setNames(SeoulcombinedROItable[19:81], list_FA))
# MD
which(colnames(SeoulMD) == "ACR.md")
ncol(SeoulMD)
SeoulMD <- SeoulMD[1] %>%
bind_cols(setNames(SeoulMD[2:64], list_MD))
# RD
which(colnames(SeoulRD) == "ACR.RD")
ncol(SeoulRD)
SeoulRD <- SeoulRD[1] %>%
bind_cols(setNames(SeoulRD[2:64], list_RD))
# AD
which(colnames(SeoulAD) == "ACR.AD")
ncol(SeoulAD)
SeoulAD <- SeoulAD[1] %>%
bind_cols(setNames(SeoulAD[2:64], list_AD))
#### 11. Seoul - Arrange ####
SeoulcombinedROItable <- SeoulcombinedROItable %>%
arrange(subjectID)
SeoulMD <- SeoulMD %>%
arrange(subjectID)
SeoulRD <- SeoulRD %>%
arrange(subjectID)
SeoulAD <- SeoulAD %>%
arrange(subjectID)
#### 11. Seoul - Merge ####
Seoul_merged <- SeoulcombinedROItable %>%
bind_cols(SeoulMD %>% select(-c(subjectID))) %>%
bind_cols(SeoulRD %>% select(-c(subjectID))) %>%
bind_cols(SeoulAD %>% select(-c(subjectID)))
Seoul_merged
#######################################################################
#### Merging across site ####
#######################################################################
# 1. Add Site variable
Amsterdam_merged$Site <- "Amsterdam"
Bangalore_merged$Site <- "Bangalore"
Capetown_merged$Site <- "Capetown"
Kyoto_merged$Site <- "Kyoto"
Milan_merged$Site <- "Milan"
Mountsinai_merged$Site <- "Mountsinai"
Munich_merged$Site <- "Munich"
Rome_merged$Site <- "Rome"
Saopaulo_merged$Site <- "Saopaulo"
Shanghai_merged$Site <- "Shanghai"
Seoul_merged$Site <- "Seoul"
table(Amsterdam_merged$Site)
table(Bangalore_merged$Site)
table(Capetown_merged$Site)
table(Kyoto_merged$Site)
table(Milan_merged$Site)
table(Mountsinai_merged$Site)
table(Munich_merged$Site)
table(Rome_merged$Site)
table(Saopaulo_merged$Site)
table(Shanghai_merged$Site)
table(Seoul_merged$Site)
#######################################################################
# save data
#######################################################################
setwd("../ENIGMA-OCD/0.Data/1_Site별 merged")
Amsterdam_merged <- Amsterdam_merged %>% relocate(subjectID, Site)
Bangalore_merged <- Bangalore_merged %>% relocate(subjectID, Site)
Capetown_merged <- Capetown_merged %>% relocate(subjectID, Site)
Kyoto_merged <- Kyoto_merged %>% relocate(subjectID, Site)
Milan_merged <- Milan_merged %>% relocate(subjectID, Site)