OHperSNP: Estimate Genotyping Error Rate

In sequoia: Pedigree Inference from SNPs

Estimate Genotyping Error Rate

Description

Estimate genotyping error rate from Mendelian errors per SNP.

Usage

OHperSNP(GenoM, Par, Dups = NULL)

Arguments

GenoM	genotype matrix, in sequoia's format: 1 column per SNP, 1 row per individual, genotypes coded as 0/1/2/-9, and rownames giving individual IDs.
Par	pedigree dataframe, only genotyped parents are used.
Dups	pairs of duplicates

Value

A dataframe with columns:

n.dam, n.sire, n.pair	Number of dams, sires, parent-pairs successfully genotyped for the SNP
OHdam, OHsire	Count of number of opposing homozygous cases
MEpair	Count of Mendelian errors, includes opposing homozygous cases
n.dups, n.diff	Number of duplicate pairs successfully genotyped for the SNP; number of differences

See Also

SnpStats.

sequoia documentation built on Sept. 8, 2023, 5:29 p.m.