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Convert HLA Alleles to Serological Equivalents

Source: R/toSerology.R
toSerology.Rd

Converts HLA alleles in IMGT/HLA nomenclature (e.g., "A*01:01") to their serological equivalents (e.g., "A1") using WMDA standard nomenclature.

Usage

toSerology(
  x,
  locus = NULL,
  resolve_splits = TRUE,
  return = c("serology", "genotype", "data.frame"),
  na_action = c("NA", "warn", "error")
)

Arguments

x

Character vector of HLA alleles OR an hla_genotype object.

locus

Optional character. Override locus detection for ambiguous cases.

resolve_splits

Logical. If TRUE (default), attempts to infer split antigens from broad antigens (e.g., DR2 -> DR15 or DR16 based on the allele).

return

Character. Output format:

  • "serology" (default): Returns character vector of serology strings

  • "genotype": Returns hla_genotype with *_ser_* columns added

  • "data.frame": Returns data.frame with allele, locus, serology columns

na_action

Character. How to handle alleles without serology mapping:

  • "NA" (default): Return NA for unknown alleles

  • "warn": Return NA and issue a warning

  • "error": Stop with an error

Value

Depends on return parameter. See above.

Details

This function uses the WMDA (World Marrow Donor Association) nomenclature files to map HLA alleles to their serological equivalents. The mapping considers:

  • Unambiguous assignments (highest priority)

  • Possible assignments

  • Assumed assignments

  • Expert assignments

When resolve_splits = TRUE, broad antigens like DR2 are resolved to their split antigens (DR15 or DR16) based on the specific allele.

P-group notation (e.g., "A*01:01P") is automatically resolved to the reference allele.

Examples

# Single allele conversion
toSerology("A*01:01")
#> [1] "A1"

# Vector of alleles
toSerology(c("A*01:01", "B*07:02", "DRB1*03:01"))
#> [1] "A1"   "B7"   "DR17"

# Get detailed data.frame
toSerology(c("A*01:01", "B*07:02"), return = "data.frame")
#>    allele locus allele_2f serology serology_full
#> 1 A*01:01     A     01:01        1            A1
#> 2 B*07:02     B     07:02        7            B7

# With hla_genotype object
geno <- hlaGeno(data.frame(
  A_1 = "A*01:01", A_2 = "A*02:01",
  B_1 = "B*07:02", B_2 = "B*08:01",
  stringsAsFactors = FALSE
))
toSerology(geno, return = "serology")
#> A*01:01 A*02:01 B*07:02 B*08:01 
#>    "A1"    "A2"    "B7"    "B8" 
toSerology(geno, return = "genotype")
#> HLA Genotype Data
#> -----------------
#> Loci present: A, B 
#> Number of samples: 1 
#> 
#>       A_1     A_2     B_1     B_2 A_ser_1 A_ser_2 B_ser_1 B_ser_2
#> 1 A*01:01 A*02:01 B*07:02 B*08:01      A1      A2      B7      B8