Run collider bias assessment

Usage

collider_bias(
  x,
  bias_method = "dudbridge",
  r2 = 0.001,
  p1 = 5e-08,
  kb = 250,
  plink2 = genepi.utils::which_plink2(),
  plink_ref = genepi.utils::which_1000G_reference(build = "GRCh37"),
  ip = 0.001,
  pi0 = 0.6,
  sxy1 = 1e-05,
  bootstraps = 100,
  weighted = TRUE,
  method = "Simex",
  B = 1000,
  seed = 2023
)

Arguments

x: an object of class MR
bias_method: a character or character vector, one or more of c("dudbridge", "slopehunter", "mr_ivw", "mr_egger", "mr_weighted_median", "mr_weighted_mode")
r2: a numeric 0-1, r2 used for clumping - set all clumping params to NA to turn off
p1: a numeric 0-1, p1 used for clumping - set all clumping params to NA to turn off
kb: an integer, kb used for clumping - set all clumping params to NA to turn off
plink2: a path, the plink2 binary
plink_ref: a path, the reference genome pfile
ip: a numeric 0-1, threshold for removing incidence variants; see xp_thresh SlopeHunter::hunt()
pi0: a numeric 0-1, proportion of SNPs in the incidence only cluster; see init_pi SlopeHunter::hunt()
sxy1: a numeric, the covariance between incidence and progression Gip SNPs; see init_sigmaIP SlopeHunter::hunt()
bootstraps: an integer, number of bootstraps to estimate SE; see M SlopeHunter::hunt()
weighted: see weighted indexevent::indexevent()
method: see method indexevent::indexevent()
B: see B indexevent::indexevent()
seed: seed, for reproducibility