| hothiphop {hiphop} | R Documentation |
A function that calculates the genetic mismatches according to the hiphop and hot test
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, martijn@myscience.eu
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)