topmatch: A function selecting the dams and sires with the fewest...

In hiphop: Parentage Assignment using Bi-Allelic Genetic Markers

Description

This function summarizes per offspring the top combinations of dam and sire that have the least genetic mismatches according to the hot (Huisman 2017) and/or hiphop (Cockburn et al. in revision) test criteria. In addition to the top matched combinations the summary always also list the social parent, if not among the top X. The user can choose whether one wants to look for the most likely dam and sire with and without assuming that the social mother (or father) is the genetic parent. Furthermore, one can choose on which test score to rank individuals. For more information and worked examples, see the vignette and Cockburn et al. (in revision).

Usage

topmatch(
  x,
  ranking,
  condition = "none",
  thres = 99999,
  top = 3,
  unique = "pair"
)

Arguments

x	The file with hot and hiphop scores that is generated by the 'hothiphop()' function.
ranking	This sets the mismatch criterion in which dams and sires are ranked, possibilities include ranking="hothiphop.parents", "hiphop", "hot.parents", hot.dam", "hot.sire", "hothiphop.dam", "hothiphop.sire". In some situations it can be useful to supply two ranking criteria, for example to avoid ties (e.g. ranking=c("hot.dam", "hiphop))
condition	Whether or not one wants to condition on either the social mother (condition="mother") or social father (condition="father"). The default is condition="none" in which case all possible dams and sires are considered as genetic parents.
thres	Sets a threshold value for the number of mismatches, if parents have less mismatches then the variable below.threshold in the output will have a value of 1. If 0>=thres<1, the number of mismatches will be re-expressed as a proportion of all loci sampled (not NA). If -1>thres<0 the mismatch scores are expressed as the number of mismatched divided by the number of loci at which the offspring is heterozygote (for the HIPHOP test) or divided by number of loci at which the offspring is homozygote (for the HOT test). This standardization may be sometimes useful for the recalculating the HIPHOP score to account for the fact that some offspring can be scored at more loci than others for this test. By default thres is set to a large integer (99999).
top	Sets the number of top matches that is shown in the output #' @return a dataframe with for each offspring the top X (default top 3, giving 3 rows for each offspring) dam and 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. In addition to the top X offspring-dam-sire with the fewest mismatches, the scores of the social parents are also always listed (if they were not already in the top X ranking). #' 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 rank the ranking among all possible combinations of offspring and potential dams and sires, rank 1 is fewest mismatches according to criterion chosen in the function argument 'ranking' dam an identifier of the potential dam sire an identifier of the potential sire dam.type description of the type of potential dam (social parent, extra-group parent, within-group subordinate) sire.type description of the type of potential sire (social parent, extra-group parent, within-group subordinate) 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 below.threshold if the score chosen in argument 'ranking' is below the chose threshold value, then equals to 1, else 0 threshold the chosen threshold value in argument 'threshold' 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 the 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 social.mother identity of the social mother of the offspring social.father identity of the social father of the offspring condition the value of the argument 'condition' ranking the value of the (first) value in the argument 'ranking' ranking2 the value of the second value in the argument 'ranking'
unique	When using the ranking criteria hot.dam or hot.sire the best ranked dam or sire will occupy the entire top 3 and this does not allow comparing among dams. By setting unique to "dam" (or "sire") the output shows the top 3 with the best record for each unique dam (or sire).

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)
best<-topmatch(x=results, ranking="hothiphop.parents")
head(best)

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