mendelianCheck: Check for Mendelian errors

In magnusdv/pedtools: Creating and Working with Pedigrees and Marker Data

Check for Mendelian errors

Description

Check marker data for Mendelian inconsistencies

Usage

mendelianCheck(x, remove = FALSE, verbose = !remove)

Arguments

x	a ped() object
remove	a logical. If FALSE, the function returns the indices of markers found to incorrect. If TRUE, a new ped object is returned, where the incorrect markers have been deleted.
verbose	a logical. If TRUE, details of the markers failing the tests are shown.

Value

A numeric containing the indices of the markers that did not pass all tests, or (if remove = TRUE) a new ped object where the failing markers are removed.

Author(s)

Magnus Dehli Vigeland

Examples

x = nuclearPed()

# Add a SNP with Mendelian error
m = marker(x, '1' = "1/1", '2' = "1/1", '3' = "1/2")
x = setMarkers(x, m)

mendelianCheck(x)

magnusdv/pedtools documentation built on April 9, 2024, 7:35 a.m.