Per-Gene Variant-Pruning Settings

Which variants survive into each gene's weight matrix before cTWAS sees it. maxVariants caps the count; csMinCor and pipRescue mark variants as must-keep so they survive the cap.

Usage

VariantPruningParam(
  weightCutoff = 0,
  csMinCor = 0.8,
  pipRescue = 0,
  maxVariants = Inf
)

Arguments

weightCutoff

Numeric. Drop variants with |weight| < weightCutoff. Default 0 (no filter).

csMinCor

Numeric. Variants in a 95% credible set whose purity (min_abs_corr) is at least this are must-keep. Default 0.8. Requires a fineMappingResult; ignored without one.

pipRescue

Numeric. Variants with PIP above this are must-keep. Default 0 (no PIP rescue). Requires a fineMappingResult.

maxVariants

Numeric. Cap on the per-gene variant count. Above it, all must-keep variants are retained and the remaining slots filled by descending PIP (when available) or descending |weight|. Default Inf (no cap).

Value

A VariantPruningParam object, a MethodParam.

Examples

VariantPruningParam(weightCutoff = 1e-4, maxVariants = 5000)
#> <VariantPruningParam>
#>   weightCutoff             1e-04
#>   csMinCor                 0.8
#>   pipRescue                0
#>   maxVariants              5000