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Summary-Statistic Row Filtering Options

Source: R/sumstatsQc.R
SumstatsFilterParam.Rd

Which rows of a summary-statistics table survive QC, as one checked bundle. These act on the sumstats themselves, not on any genotype matrix, which is why they are separate from GenotypeFilterParam.

Usage

SumstatsFilterParam(
  removeIndels = FALSE,
  removeStrandAmbiguous = TRUE,
  infoCutoff = 0,
  nCutoff = 5
)

Arguments

removeIndels

Logical. Drop insertions and deletions. Default FALSE.

removeStrandAmbiguous

Logical. Drop strand-ambiguous variants (A/T and C/G). Default TRUE.

infoCutoff

Imputation-INFO floor. Default 0.

nCutoff

Per-variant sample-size floor. Default 5.

Value

A SumstatsFilterParam object, a MethodParam.

See also

GenotypeFilterParam, PanelFilterParam

Examples

SumstatsFilterParam(removeIndels = TRUE, infoCutoff = 0.8)
#> <SumstatsFilterParam>
#>   removeIndels             TRUE
#>   removeStrandAmbiguous    TRUE
#>   infoCutoff               0.8
#>   nCutoff                  5