Get SLALOM / DENTIST Diagnostics

Return the per-variant LD-mismatch diagnostics table (SLALOM or DENTIST output) attached to a sumstats entry by summaryStatsQc when zMismatchQc was not "none". Convenience accessor over getQcInfo(x)$entryAudit[[entry]]$ldMismatchDiagnostics.

Usage

getQcDiagnostics(x, entry = 1L, ...)

# S4 method for class 'SumStatsBase'
getQcDiagnostics(x, entry = 1L, ...)

Arguments

x

A GwasSumStats or QtlSumStats object.

entry

Integer index (default 1) of the entry whose diagnostics table to return. When NULL, returns a named list of every entry's diagnostics keyed by entry index.

...

Unused.

Value

A data.frame of per-variant diagnostics (columns include variant_id plus the SLALOM / DENTIST output columns), NULL when no diagnostics were preserved for that entry, or a named list of such data.frames when entry = NULL.

Examples

data(qtlSumStatsExample)
getQcDiagnostics(qtlSumStatsExample)
#> NULL