Metabolomics QC for DoD project

Note that this pipeline is for reference rather than for use. Some code will not work out-of-the-box, as it includes code for wrangling data that was in a non-standard format.

The code that is the most reusable is 02_qc_mets.R, which accepts metabolite measurement data with metabolites as rows, samples as columns.

Data was not pushed to GitHub as it is restricted-access, but examples of what it looked like are given below.

Scripts

• 00_install_pkgs.R: installs required R packages.
• 01_preprocess_mets.R: Takes the raw data that was in non-standard format, extracts metabolite metadata, sample metadata, and metabolite measurements. Example below:
  • Raw data:

 |         |          |          |      |                           | Date extracted        | MM/DD/YY | MM/DD/YY
 |         |          |          |      |                           | Date injected         | MM/DD/YY | MM/DD/YY
 |         |          |          |      |                           | Column                | 1        | 1
 |         |          |          |      |                           | Analysis order        | 2        | 3
 | Method  | Compound | m/z      | RT   | HMDB ID (*representative) | Metabolite            | TOM###1  | TOM###2
 | HIL-pos | QI221    | 126.1369 | 7.45 | Internal Standard         | valine-d8             | 41368    | 42225
 | HIL-pos | QI197    | 174.1371 | 6.75 | Internal Standard         | phenylalanine-d8      | 136352   | 139558
 | HIL-pos | QI2      | 197.0677 | 3.58 | HMDB11103                 | 1.7-dimethyluric acid | 5141     | 648

• Extracted metabolite metadata:

| Method  | Compound | m/z      | RT   | HMDB ID
| HIL-pos | QI221    | 126.1369 | 7.45 | Internal Standard         
| HIL-pos | QI197    | 174.1371 | 6.75 | Internal Standard         
| HIL-pos | QI2      | 197.0677 | 3.58 | HMDB11103                 

• Extracted sample metadata:

extraction_date | injection_date | column | analysis_order | sample_id
MM/DD/YY        | MM/DD/YY       | 1      | 2              | TOM###1
MM/DD/YY        | MM/DD/YY       | 1      | 3              | TOM###2

• Extracted measurement data:

           TOM###1 | TOM###2
QI221_hn | 41368   | 42225
QI197_hn | 136352  | 139558
QI2_hn   | 5141    | 649

• 02_qc_mets.R: Performs QC on the formatted measurement data. Steps:
  • Remove metabolite with 0 variance
  • Remove metabolites with >25% missingness
  • Remove samples with >25% missingness
  • Apply various transformations to the data
  • Winsorize to the 5th standard deviation
  • Batch adjustment by median-scaling to a reference batch
• 03_merge_mets.R: There were separate files for each LC-MS method (C8-positive, HILIC-positive, Amines, see here). This script merges the methods together.