/PPMI_Data_Wrangling

Primary LanguageR

PPMI_Data_Wrangling

Overview

Gets raw PPMI data -> outputs processed/cleaned versions

Required Libraries (& Versions)

R: 4.2.1 (2022-06-23)
library(tidyr): 1.2.1
library(dplyr): 1.1.0
library(reshape2): 1.4.4
library(hablar): 0.3.1
library(data.table): 1.14.6
library(stringr): 1.5.0



Steps

Step 1: Createa new folder & put the following 11 or 12 files/scripts inside it

  1. PPMI_Wide_to_Cleaned.R
  2. PPMI_Wide_to_Cleaned_Imaging.R
  3. PPMI_Cleaned_to_Processed.R
  4. PPMI_Wide_to_Processed_Bio.R
  5. PPMI_Cleaned_to_Processed_Imaging.R
  6. PPMI_Wrapper.R
  7. PPMI_Merge_Final.R
  8. PPMI_Raw_to_Wide.R
  9. UPSIT_to_percentile.R
  10. UPSIT_Normative_Values_female.csv
  11. UPSIT_Normative_Values_male.csv
  12. OPTIONAL: PPMI_CNO.csv
    12.1 if you want to add CNO, create a file with unique patient IDs as column 1 and CNO numbers as column 2
    12.2 if CNO is not needed, comment the "Add CNOs" section out in the PPMI_Cleaned_to_Processed.R file

Step 2: Run PPMI_Wrapper.R



Final Useful Files

Behavioral

PPMI_allVisits_cleaned_processed.csv
PPMI_extraVisits_cleaned_processed.csv
PPMI_regularVisits_cleaned_processed.csv
NOTE: Regular Visit include BL and Uxx visits. Extra Visit included everything in All Visit except the regular Visit ones.

Imaging

PPMI_Imaging_All_cleaned_processed.csv
PPMI_Imaging_Main_cleaned_processed.csv
NOTE: "PPMI_Imaging_Main_cleaned_processed.csv" has the imaging information that is used in "Merged_Final" files"

Behavioral + Imaging

PPMI_Merged_FINAL_AllVisits.csv
PPMI_Merged_FINAL_ExtraVisits.csv
PPMI_Merged_FINAL_RegularVisits.csv
NOTE: Regular Visit include BL and Uxx visits. Extra Visit included everything in All Visit except the regular Visit ones.

Bio

PPMI_Bio_cleaned_processed.csv