How lucivargas/prs_calibration_la works
PRS_calibration_LA is a command-line workflow for calibrating polygenic risk scores (PRS) using local ancestry. The numbered scripts suggest stages for checking inputs, obtaining and preparing score/variant data, applying reference and target scores, matching local ancestry to PRS, and running simulations and summaries. The README confirms the product purpose but does not document script invocation or data flow; dashed links therefore indicate only a possible order inferred from filenames, not verified calls.
Main entry points: 10_simulations.R Run simulations · 01_check_requirements.sh Check requirements · 02_check_target.R Check target · 03_download_score.sh Download scores
Components 17
Input and variant preparation
- Check requirements
Functions/01_check_requirements.sh - Check target
Functions/02_check_target.R - Download scores
Functions/03_download_score.sh - Extract variants
Functions/04_extract_variants.sh - Find overlaps
Functions/05_find_overlapping_variants.R
GWAS and score processing
- Process GWAS
Functions/06_01_process_gwas.R - Filter data
Functions/06_filter_data.sh - Apply reference PRS
Functions/07_apply_pgs_ref.R - Apply target PRS
Functions/08_apply_pgs_target.R
Local ancestry calibration
- Match LAI to PRS
Functions/09_match_lai_to_prs.R
Simulation and summaries
- Run simulations
Functions/10_simulations.R - Average LAI
Functions/11_average_lai.R - Calculate percentiles
Functions/11_calculate_percentiles.R - Shared utilities
Functions/utils.R
Other components
- User
- Calibration runner
calibrate_prs.sh - Configuration
config.yml
Connections 14
- User → Calibration runner: invokes?
- Calibration runner → Check requirements: may run
- Check requirements → Check target: possible next
- Check target → Download scores: possible next
- Download scores → Extract variants: possible next
- Extract variants → Find overlaps: possible next
- Find overlaps → Process GWAS: possible next
- Process GWAS → Filter data: possible next
- Filter data → Apply reference PRS: possible next
- Apply reference PRS → Apply target PRS: possible next
- Apply target PRS → Match LAI to PRS: possible next
- Match LAI to PRS → Run simulations: possible next
- Run simulations → Average LAI: possible next
- Run simulations → Calculate percentiles: possible next