mendel.distance: Compute rate of Mendelian inconsistency between an individual...

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Compute rate of Mendelian inconsistency between an individual and possible mother-father pairs.

Usage

mendel.distance(gty, parents, verbose = TRUE, ...)

Arguments

gty	a genotypes object containing exactly one target individual
parents	a genotypes object containing possible parents for the target individual
verbose	logical; if TRUE, send progress messages to terminal
...	ignored

Details

Define the "Mendel distance" between an individual and two possible parents as the mean rate of Mendelian inconsistencies – that is, markers at which zero alleles are shared IBS between one parent and one offspring – across the pairs (father, offspring) and (mother, offspring). Given a set of possible parents (in parents), this function creates all possible male-female pairs and computes the Mendel distance between each pair and a single target individual (in gty).

If the sex of the target individual is non-missing, the sex chromosomes will be handled specially: for males, chrY is compared to the father's chrY and chrX to the mother's chrX; for females, chrX is compared to both parents and chrY is ignored. If the sex of the target individual is missing, the sex chromosomes will be ignored, and mitochondrial markers are always ignored because they are so few in number and tend to be homoplasic.

Value

a dataframe of mother-father pairs and corresponding Mendel distances

See Also

guess.parents

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.