Flag and drop genome-wide significant lead variants that have no supporting signal from nearby variants. A genuine association is usually accompanied by correlated (LD) variants with elevated signal, so a very strong lead with no nearby support is suspicious (e.g. a genotyping artifact or a spurious rare-variant singleton). A lead is treated as aberrant when its p-value is below `lead_pvalue_threshold` and no other variant within `window_kb` kilobases on the same chromosome reaches `support_pvalue_threshold`. The number of variants that would be dropped is logged before they are removed.
Arguments
- x
A `GWASFormatter` object, `data.frame`, or `tibble`.
- ...
Additional arguments passed to methods.
- lead_pvalue_threshold
Lead variants with `PVALUE` strictly below this are examined. Default `5e-10`.
- support_pvalue_threshold
A lead is kept (supported) if any other variant within the window reaches this p-value. Default `5e-5`.
- window_kb
Distance in kilobases from the lead, on the same chromosome, searched for a supporting variant. Default `500`.