Analysis of tear fluid proteomics

Scripts to analyse proteomics data of ALS and control patients with unsupervised and supervised machine learning. Includes plotting of the results.

Analysis includes

• PCA
• UMAP
• tSNE
• heatmap
• linear regression model
• random forest model
• support vector machine model
• gene enrichment analysis

Scripts

• unsupervised.R includes PCA, UMAP, tSNE and heatmap analysis and visualisations
• fgsea.R script for Gene Set Enrichment Analysis
• functions.R script containing the functions that are used in fgsea.R and ml_github.R
• ml_github.R script containing the machine learning analysis with plotting of the results
• aucCombinations.R script containing AUC calculations based on previous run linear regression models - see analysis.md for more informations
• data_completeness.R script to analyse data completeness and calculate coefficient of variation of the raw proteomics data

Data

The data folder contains mockdata and a file with annotated KEGG pathways.