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De-identify an MHC haplotype carrier table

Source: R/obfuscateMhcHaplotypes.R
obfuscateMhcHaplotypes.Rd

Remaps the id column of a mhcHaplotypeCarriers table through the same alias vector obfuscatePed(..., map = TRUE) already returns. obfuscatePed scrubs exactly one pedigree data frame and cannot reach a second, sidecar object – this is the companion scrub an MHC carrier table needs so an "obfuscated" export never leaks real animal ids while the main pedigree is de-identified.

Usage

obfuscateMhcHaplotypes(carriers, map)

Arguments

carriers

data.frame with columns haplotype, id, uncertain as returned by mhcHaplotypeCarriers.

map

named character vector of aliases, keyed by the original id – the map element of obfuscatePed(..., map = TRUE)'s return value.

Value

carriers with id replaced by its alias; haplotype and uncertain are unchanged.

Details

Haplotype labels are left byte-identical: an MHC haplotype name is a shared nomenclature term, not an animal identifier, and there is no validity-preserving way to obfuscate one. Only id is ever remapped – a map entry whose name happens to match a haplotype label never touches the haplotype column. The uncertain disclosure column passes through unchanged.

A row whose id is absent from map stop()s rather than silently dropping or leaking the real id.

See also

mhcHaplotypeCarriers, obfuscatePed

Other obfuscation: mapIdsToObfuscated(), obfuscateDate(), obfuscateGenomicROH(), obfuscateGenotypeMatrix(), obfuscateId(), obfuscateLdBlocks(), obfuscatePed(), obfuscateTwinRelations()

Examples

ped <- data.frame(
  id = c("F1", "F2", "S1", "S2"),
  sire = c(NA, NA, "F1", "F1"),
  dam = c(NA, NA, "F2", "F2"),
  sex = c("M", "F", "F", "F"),
  stringsAsFactors = FALSE
)
genotype <- data.frame(
  id = c("S1", "S2"),
  haplotype1 = c("A001_B001", "A001_B001"),
  haplotype2 = c("A002_B012", "A008_B015b"),
  stringsAsFactors = FALSE
)
carriers <- mhcHaplotypeCarriers(genotype, rareOnly = FALSE)
obfuscated <- obfuscatePed(ped, map = TRUE)
obfuscateMhcHaplotypes(carriers, obfuscated$map)
#>    haplotype     id uncertain
#> 1  A001_B001 FCDNFK     FALSE
#> 2  A001_B001 GJGR1A     FALSE
#> 3  A002_B012 FCDNFK     FALSE
#> 4 A008_B015b GJGR1A     FALSE