Flag Mendelian-inconsistent recorded parents from marker genotypes

For each animal in pedigree with a recorded dam and/or sire that is also genotyped, compares the animal's marker genotype to that recorded parent's, locus by locus, and counts loci at which no shared allele is possible under simple Mendelian inheritance ("opposite homozygotes" – the animal and the candidate parent are each homozygous for a different allele). Aggregates to a per-pair exclusion count and a flagged decision, directly targeting the issue's named ~5% dam-misidentification problem: a recorded parent whose genotype evidence contradicts the pedigree.

Usage

markerParentageExclusion(genotypeMatrix, pedigree, maxExclusions = 2L)

Arguments

genotypeMatrix: a character matrix as returned by buildMarkerGenotypeMatrix: rows are individual ids, columns are loci, and each cell is that individual's two alleles at that locus, sorted and joined by "/" (or NA if not genotyped at that locus).
pedigree: a data frame with (at least) columns id, sire, and dam – the standard pedigree shape used throughout this package. sire/dam may be NA for an unrecorded parent.
maxExclusions: integer; the maximum number of Mendelian- inconsistent loci tolerated before a recorded parent is flagged as excluded. Default 2L (flag only at 3 or more).

Value

A data frame, one row per (offspring, recorded-parent) pair for which both individuals are genotyped, with columns id (the offspring), parentId, role ("dam" or "sire"), exclusionCount, nLoci (the number of jointly-genotyped loci the count is based on), and flagged (the canonical boolean vocabulary, matching reportGV()'s flagged column). A pair with an unrecorded or ungenotyped parent has no row at all. A data frame with zero rows (but the full column shape) is returned when no pair is checkable.

Details

A locus contributes to the exclusion count only when both the animal and the candidate parent are genotyped there and both are homozygous for different alleles – the same "informative conflict" definition verified against the ICAR/ISAG cattle-SNP parentage-verification standard at this function's Pre-RED (a heterozygous genotype at either individual is never, by itself, Mendelian-inconsistent with a biallelic parent genotype). Loci where either individual is not genotyped are excluded from both the numerator and the denominator.

maxExclusions is the maximum number of Mendelian-inconsistent loci tolerated before a recorded parent is flagged as excluded (i.e. flagging requires exclusionCount > maxExclusions) – a single mismatching locus is not, by itself, evidence the recorded parent is wrong, since ordinary genotyping error or mutation can produce an isolated conflict even for a true parent-offspring pair. The default of 2 (flag only at 3 or more inconsistent loci) is grounded in Cifuentes et al. (2006) and the real captive-macaque-colony parentage precedent of de Groot et al. (2025), both cited below – it is a raw locus count calibrated to small/moderate marker panels and typical genotyping error rates reported in that literature; it does not scale with the number of loci actually typed or with this package's (currently unmeasured) per-locus genotyping-error rate, so panels much larger or noisier than that should retune maxExclusions rather than rely on the shipped default.

When an animal and its recorded parent share zero jointly-genotyped loci, the exclusion count is undefined; that pair's exclusionCount and flagged are NA and a warning names the pair (mirroring markerKinship's precedent for the same kind of no-shared-evidence case). A recorded parent that is NA (unknown) or that has no row in genotypeMatrix (never genotyped) is silently skipped – no row is emitted for that pair, since there is no genotype evidence to check.

References

Cifuentes, L. O., Martinez, E. H., Acuna, M. P., & Jonquera, H. G. (2006). Probability of exclusion in paternity testing: time to reassess. Journal of Forensic Sciences, 51(2), 349-350. doi:10.1111/j.1556-4029.2006.00046.x

de Groot, N. G., de Vos-Rouweler, A. J. M., Heijmans, C. M. C., et al. (2025). Genetic Conservation and Population Management of Non-Human Primates: Parentage Determination Using Seven Microsatellite-Based Multiplexes. Ecology and Evolution, 15(4), e71216. doi:10.1002/ece3.71216

Examples

library(nprcgenekeepr)
markerGenotype <- data.frame(
  id = c("A", "A", "B", "B"),
  locus = c("L1", "L2", "L1", "L2"),
  allele1 = c("A", "A", "A", "A"),
  allele2 = c("A", "B", "B", "B"),
  stringsAsFactors = FALSE
)
genotypeMatrix <- buildMarkerGenotypeMatrix(markerGenotype)
pedigree <- data.frame(id = "B", sire = NA_character_, dam = "A",
                        stringsAsFactors = FALSE)
markerParentageExclusion(genotypeMatrix, pedigree)
#>   id parentId role exclusionCount nLoci flagged
#> 1  B        A  dam              0     2   FALSE