dupGenotypes: Duplicate Genotypes
In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

dupGenotypes

R Documentation

Duplicate Genotypes

Description

Identify duplicate or very similar genotypes.

Usage

dupGenotypes(g, num.shared = 0.8)

Arguments

`g`	a gtypes object.
`num.shared`	either number of loci or percentage of loci two individuals must share to be considered duplicate individuals.

Value

if no duplicates are present, the result is NULL, otherwise a data frame with the following columns is returned:

`ids.1, ids.2`	sample ids.
`strata.1, strata.2`	sample stratification.
`mismatch.loci`	loci where the two samples do not match.
`num.loci.genotyped`	number of loci genotyped for both samples.
`num.loci.shared`	number of loci shared (all alleles the same) between both samples.
`prop.loci.shared`	proportion of loci genotyped for both samples that are shared.

Author(s)

Eric Archer eric.archer@noaa.gov

Examples

data(msats.g)

# identify potential duplicates in Coastal strata
coastal <- msats.g[, , "Coastal"]
coastal.5 <- coastal[getIndNames(coastal)[1:5], , ]
dupes <- dupGenotypes(coastal.5)
dupes

EricArcher/strataG documentation built on Feb. 12, 2023, 4:11 a.m.