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LD Reference Panel Filtering Options

Source: R/ld.R
PanelFilterParam.Rd

Which of an LD panel's variants are kept before the panel is used, as one checked bundle. Narrower than GenotypeFilterParam: a panel is not a study's genotypes, so there is no sample restriction and no variance cutoff, and the missingness default is 1 (no filter) rather than 0.

Usage

PanelFilterParam(mafCutoff = 0, macCutoff = 0, imissCutoff = 1)

Arguments

mafCutoff

Minor-allele-frequency floor. Default 0.

macCutoff

Minor-allele-count floor; the stricter of this and mafCutoff applies, using the panel's real sample count – for a stochastic LD sketch, the one its .afreq records, not its pseudo-samples. Default 0.

imissCutoff

Per-variant missingness ceiling. Default 1, which filters nothing and lets the allele-frequency sidecar be read instead of materializing dosage.

Value

A PanelFilterParam object, a MethodParam.

See also

GenotypeFilterParam, SumstatsFilterParam

Examples

PanelFilterParam(mafCutoff = 0.001)
#> <PanelFilterParam>
#>   mafCutoff                0.001
#>   macCutoff                0
#>   imissCutoff              1