Docs: Multimodal integration

[lucas-diedrich]

Integrate proteomics, RNA microarray data + methylation data with MOFA+

Lehtiö, J. et al. Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune-evasion mechanisms. Nat Cancer 2, 1224–1242 (2021). PXD020191

Structure

• Read + preprocess MS-proteomics data based on original publication
• Integrate with RNA microarray + methylation data
• Run MOFA+ as factor model
• Interpret MOFA+ factor activities (plotting, separation of histological subtypes)
• Interpret MOFA+ factor loadings (specifically factor 2) with MOFA+
• Silhouette with computation as proxy for separation across modalities

Key figures

Explained variance of MOFA+ model

GSEA of factor 2

Cohort separation (single-modality vs. joint modeling)

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 72.74%. Comparing base (ca7b133) to head (6dbe6ec).
⚠️ Report is 108 commits behind head on main.

Additional details and impacted files

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- Coverage   73.19%   72.74%   -0.45%     
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  Files          35       35              
  Lines        2067     2066       -1     
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- Hits         1513     1503      -10     
- Misses        554      563       +9     

see 4 files with indirect coverage changes

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