hothiphop: A function that calculates the genetic mismatches according...

In hiphop: Parentage Assignment using Bi-Allelic Genetic Markers

Description

This function calculates the number genetic mismatches according to the hiphop and hot test for any combination of offspring-potential.dam-potential.sire. The HOT test (Homozygous Opposite Test; Huisman 2017) compares the genotype of an offspring with a potential parent: a mismatch is scored when both the offspring and parent are homozygous, but for different alleles. The HIPHOP test (Homozygous Identical Parents, Heterozygous Offspring are Precluded; Cockburn et al. in revision) compares the genotype of an offspring with both potential parents: a mismatch is scored when the offspring is heterozygous and both parent are homozygous for the same allele The resulting output can next be summarized using the 'topmatch()' function.

Usage

hothiphop(ind, gen)

Arguments

ind	The input file with individuals, which should contain at least the columns brood, individual, type, social.parent, year.
gen	The input file with genotypes, which should contain the loci-names as column headers and the individual names as row-header and should only contain the values 0, 1, 2 or NA.

Value

a dataframe with all possible offspring-potential.dam-potential.sire combinations and their mismatch scores according to the HOT and HIPHOP test, the number of loci this was based on, and some additional relevant information about the social parents and potential dam and sires

year

the year or cohort that is being considered, adults can be potential dam or sire in some years, but no in others

brood

an identifier of the brood to which the offspring and adults belong/are associated with

offspring

an identifier of the offspring

potential.dam

an identifier of the potential dam

potential.sire

an identifier of the potential sire

hothiphop.parents

the sum of the hiphop and hot.parents mismatch score

hiphop

the hiphop mismatch score of the offspring with the potential dam and potential sire, expressed as the number of loci giving mismatches

hot.parents

the hot score of the offspring with both the potential dam and sire, expressed as the number of loci giving mismatches

hot.dam

the hot score of the offspring with the potential dam, expressed as the number of loci giving mismatches

hot.sire

the hot mismatch score of the offspring with the potential sire , expressed as the number of loci giving mismatches

hothiphop.dam

the sum of the hot.dam and hiphop mismatch score

hothiphop.sire

the sum of the hot.sire and hiphop mismatch score

loci.dyad.dam

the number of loci at which both the offspring and dam were not NA

loci.dyad.sire

the number of loci at which both the offspring and sire were not NA

loci.triad

the number of loci at which the offspring, dam and sire were not NA

offspring.heterozygosity

proportion of loci at which the offspring was heterozygous

social.mother.sampled

if the social.mother genotypic data is in the genotypes file then equal to 1, else 0

social.father.sampled

if the social.father genotypic data is in the genotypes file then equal to 1, else 0

is.dam.social

if the potential dam is the social mother then equal to 1, else 0

is.sire.social

if the potential sire is the social father then equal to 1, else 0

is.dam.within.group

if the potential dam is part of the same group (i.e. associated with the same brood) as the offspring, then equal to 1, else 0

is.sire.within.group

if the potential sire is part of the same group (i.e. associated with the same brood) as the offspring, then equal to 1, else 0

social.mother

identity of the social mother of the offspring

social.father

identity of the social father of the offspring

Author(s)

Martijn van de Pol, [e-mail]

Source

Cockburn et al. (2020) HIPHOP: improved paternity assignment among close relatives using a simple exclusion method for biallelic markers. Molecular Ecology Resources, in revision.

References

Cockburn et al. (2020) HIPHOP: improved paternity assignment among close relatives using a simple exclusion method for biallelic markers. Molecular Ecology Resources, in revision.

Huisman, J. (2017). Pedigree reconstruction from SNP data: parentage assignment, sibship clustering and beyond. Molecular ecology resources, 17(5), 1009-1024.

Examples

results<-hothiphop(ind=individuals[1:22,], gen=genotypes)
head(results)
best<-topmatch(x=results, ranking="hothiphop.parents")
head(best)

hiphop documentation built on Aug. 19, 2020, 5:07 p.m.