bio-causal-genomics-pleiotropy-detection

MR-PRESSO

Goal: Detect and remove pleiotropic outlier instruments from an MR analysis.

Approach: Run MR-PRESSO to test for global pleiotropy, identify individual outlier SNPs, test whether their removal changes the causal estimate (distortion test), and obtain a corrected estimate.

## Columns needed: beta.exposure, beta.outcome, se.exposure, se.outcome

presso_input <- data.frame(
  bx = dat$beta.exposure,
  by = dat$beta.outcome,
  bxse = dat$se.exposure,
  byse = dat$se.outcome
)

## SignifThreshold: P-value threshold for outlier detection (0.05 standard)

presso_result <- mr_presso(
  BetaOutcome = 'by', BetaExposure = 'bx',
  SdOutcome = 'byse', SdExposure = 'bxse',
  OUTLIERtest = TRUE, DISTORTIONtest = TRUE,
  data = presso_input,
  NbDistribution = 5000,
  SignifThreshold = 0.05
)