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Additional Arguments For plinkQC::relatednessFilter

Source: R/relatednessQc.R
PlinkQcOptions.Rd

The secondary-criterion settings filterRelatedness forwards to plinkQC::relatednessFilter, plus anything else that function accepts. Names are plinkQC's own and are checked against plinkQC::relatednessFilter's live formals, so the check cannot drift from the upstream signature. See MethodOptions for when checking is not possible.

The pair identifiers, the relatedness column and the threshold are not settable here: filterRelatedness derives those from its own columns and relatednessThreshold arguments, which its graph pre-pruning uses as well, and injects them.

Usage

PlinkQcOptions(
  otherCriterion = NULL,
  otherCriterionTh = NULL,
  otherCriterionThDirection = "ge",
  otherCriterionIID = "IID",
  otherCriterionMeasure = NULL,
  ...
)

Arguments

otherCriterion

Optional data frame of additional filtering criteria.

otherCriterionTh

Threshold for the additional criterion.

otherCriterionThDirection

Direction of the threshold comparison. Default "ge".

otherCriterionIID

Column name for the individual ID in otherCriterion. Default "IID".

otherCriterionMeasure

Column name for the criterion measure.

...

Any other plinkQC::relatednessFilter argument.

Value

A MethodOptions object.

Examples

PlinkQcOptions(otherCriterionThDirection = "le")
#> <MethodOptions: plinkQC::relatednessFilter>
#>   forwarded to plinkQC::relatednessFilter()
#>   argument names checked against plinkQC::relatednessFilter()
#>   otherCriterionThDirection le
#>   otherCriterionIID      IID