Arguments For The SLALOM LD-Mismatch Check

Options for slalom, pecotmr's SLALOM implementation. Every field is a formal of that function, so an unknown name is rejected by R as an unused argument; there is no ... because the contract is complete. Pass the result as ldMismatchQc(method = ) or summaryStatsQc(ldMismatchQcMethod = ).

Usage

SlalomParam(
  standardError = NULL,
  abfPriorVariance = 0.04,
  nlog10pDentistSThreshold = 4,
  r2Threshold = 0.6,
  leadVariantChoice = "pvalue"
)

Arguments

standardError

Per-variant standard errors. NULL (default) leaves slalom's own data-dependent default in place.

abfPriorVariance

Prior variance for the approximate Bayes factor. Default 0.04.

nlog10pDentistSThreshold

-log10(p) threshold on the DENTIST-S statistic above which a variant is an outlier. Default 4.0.

r2Threshold

Minimum r-squared with the lead variant for a variant to be tested. Default 0.6.

leadVariantChoice

How the lead variant is chosen. Default "pvalue".

Value

A SlalomParam object, a MethodParam.

Examples

SlalomParam(r2Threshold = 0.8)
#> <SlalomParam>
#>   abfPriorVariance         0.04
#>   nlog10pDentistSThreshold 4
#>   r2Threshold              0.8
#>   leadVariantChoice        pvalue
#>   unset: standardError