Mendelian-Randomization Settings — MrParam-class • pecotmr

How causalInferencePipeline runs MR from a tuple's topLoci table.

Usage

MrParam(
  method = c("ivwPerVariant", "csAware"),
  pipCutoff = 0.5,
  cpipCutoff = 0.5,
  pvalCutoff = 1
)

Arguments

method: "ivwPerVariant" (default) filters topLoci variants by pip > pipCutoff and IVW-pools their Wald ratios. "csAware" groups variants by credible set and computes a PIP-weighted composite Wald ratio per set, using cpipCutoff.
pipCutoff: Numeric. PIP threshold for a variant to be used as an instrument. Default 0.5. Used only by "ivwPerVariant".
cpipCutoff: Numeric. Cumulative-PIP cutoff for retaining a credible set. Default 0.5. Used only by "csAware".
pvalCutoff: Numeric. MR runs for a (qtl tuple, gwas) pair only when its twasPval is below this; otherwise the MR columns are NA. Default 1 (no gate).

Value

A MrParam object, a MethodParam.

Examples

MrParam(method = "csAware", cpipCutoff = 0.8)
#> <MrParam>
#>   method                   csAware
#>   pipCutoff                0.5
#>   cpipCutoff               0.8
#>   pvalCutoff               1