https://github.com/kechrislab/combat_dogbrainmri
https://github.com/kechrislab/combat_dogbrainmri
Last synced: 9 days ago
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- Host: GitHub
- URL: https://github.com/kechrislab/combat_dogbrainmri
- Owner: KechrisLab
- License: gpl-3.0
- Created: 2021-12-10T21:17:38.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2022-06-10T17:37:45.000Z (about 4 years ago)
- Last Synced: 2025-12-25T22:26:13.001Z (6 months ago)
- Language: R
- Size: 68.4 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
# ComBat_DogBrainMRI
This repository contains the R-codes for the analyses, tables, and figures presented in the manuscript entitled "MRI data harmonization across sites using ComBat enhances classification of meningioma and glioma brain tumors in dogs: a case study" by Nandy et al., 2021+ (manuscript under review).
## R scripts
1. 3clinLowerUpper_RF_SMOTE_75iters_050321.R
Case 0 pre-ComBat lower bounds and upper bounds; no ComBat harmonization involved; only three clinical covariates in the RF model
2. 3imgVars_prepostComBat_051021.R
Pre-ComBat lower bounds, Case 1 scenarios a and b post-ComBat lower bounds, and upper bounds; only three image variables in the RF model
3. ComBat_3img3clin_050721.R
Case 1 scenarios c and d post-ComBat lower bounds; three image variables and three clinical covariates in the RF model
4. preComBat_3img3clin_LowerUpper_050721.R
Pre-ComBat lower bounds and upper bounds; three image variables and three clinical covariates in the RF model
5. ComBat_Scenario3_allcovs_090321.R
Case 2, scenarios a-d, post-ComBat lower bounds
6. Figures.R
Codes generating Figures 1, S2-S7
7. TableS6Case1_Case0.R
Codes generating the entries of and performing comparisons within Tables 1 and S6 (Case 1) and comparisons among Case 0 and Case 1 scenarios
8. TableS7_Case2.R
Codes generating the entries of and performing comparisons within Table S7 (Case 2)
9. dataPreprocessing_CCTSIproject_Final.R
Codes for preprocessing the original data to create: (1) the final data frames that are used for analyses in Cases 0, 1, and 2 and (2) the entries for Tables S1-S3
## RData files
All the RData files required to run the above scripts are available within this OneDrive folder: https://olucdenver-my.sharepoint.com/:f:/g/personal/debmalya_nandy_cuanschutz_edu/EvumZKP_09FAoLusQBQSJagBBv7xLUn74_86ZeuQByVptA?e=j4u6w0 (passcode: dogMRI@CCTSI2021)