List the animals carrying each MHC haplotype

Builds the carrier detail table for a wide per-animal MHC haplotype designation file (the checkMhcHaplotypeFile format): one row per (haplotype x carrying animal), so a colony manager can go from "which haplotypes are rare" (mhcHaplotypeFrequency's summary) to "which animals do I manage." A homozygous animal appears once per haplotype. The haplotype universe is the summary's – the distinct certain haplotypes – so a label observed only as uncertain calls has no carrier rows, matching the summary's own exclude-and-disclose rule.

Usage

mhcHaplotypeCarriers(
  genotype,
  rareOnly = TRUE,
  rareFrequencyThreshold = 0.01,
  rareCarrierThreshold = 2L
)

Arguments

genotype: dataframe with wide-format MHC haplotype data as validated by checkMhcHaplotypeFile (which this function re-runs defensively): columns id, haplotype1, haplotype2, one row per animal.
rareOnly: logical; when TRUE (the default) only the haplotypes mhcHaplotypeFrequency flags rare at the given thresholds are listed, when FALSE every summary haplotype is.
rareFrequencyThreshold: single non-negative number, passed to mhcHaplotypeFrequency. Default 0.01.
rareCarrierThreshold: single non-negative number, passed to mhcHaplotypeFrequency. Default 2L.

Value

A dataframe with columns haplotype (character), id (character), and uncertain (logical), one row per (haplotype x carrying animal), ordered by haplotype then id.

Details

The uncertain column is a per-(haplotype x animal) disclosure: FALSE when the animal has at least one certain call of that haplotype, TRUE when its carriage is only provisional (every call it has of that haplotype carries the trailing-? uncertain marker). Provisional carriers are listed here – for a rare haplotype, a provisionally typed carrier is exactly what a manager wants to see – but they are never counted in mhcHaplotypeFrequency's nCarriers or its rare-flag arithmetic. Retaining animals that carry rare variants is a distinct management objective from maintaining heterozygosity (Allendorf 1986; Lacy, Ballou & Pollak 2012), which is what a per-animal carrier list is for.

References

Allendorf, F. W. (1986). Genetic drift and the loss of alleles versus heterozygosity. Zoo Biology, 5(2), 181-190. doi:10.1002/zoo.1430050212

Lacy, R. C., Ballou, J. D., & Pollak, J. P. (2012). PMx: software package for demographic and genetic analysis and management of pedigreed populations. Methods in Ecology and Evolution, 3(2), 433-437. doi:10.1111/j.2041-210X.2011.00148.x

Examples

library(nprcgenekeepr)
## Carriers of the rare haplotypes, at the default thresholds
rareCarriers <- mhcHaplotypeCarriers(rhesusGenotypes)
head(rareCarriers)
#>     haplotype     id uncertain
#> 1 A002a_B001a BNHC69     FALSE
#> 2 A002a_B001a K93DCQ     FALSE
#> 3 A002a_B012b 6XRGWW     FALSE
#> 4 A002a_B015a 4A4EC5     FALSE
#> 5 A002a_B024a FHHNGA     FALSE
#> 6 A002a_B069a 7UMJ31     FALSE
## Every haplotype's carriers
allCarriers <- mhcHaplotypeCarriers(rhesusGenotypes, rareOnly = FALSE)