Calculate Eplet Load Between Donor and Recipient Genotypes

Aggregates **donor-specific eplets** (present in donor, absent in recipient) over loci. Can return a single total, a per-locus summary, or a pairwise recipient-vs-donor allele matrix for a chosen locus. Supports filtering by **evidence**, **exposition**, and **reactivity**.

Usage

calculateEpletLoad(
  recipient_geno,
  donor_geno,
  loci = NULL,
  evidence_level = c("A1", "A2"),
  exposition_filter = NULL,
  reactivity_filter = NULL,
  return = c("total", "per_locus", "pairwise"),
  pairwise_locus = NULL
)

Arguments

recipient_geno, donor_geno: `hla_genotype` objects.
loci: Character vector of loci to include (e.g. `c("A","B","C")`), or `NULL` (default) for all shared loci.
evidence_level: Character vector of evidence levels to include (default `c("A1","A2")`). Use `NULL` for no evidence filter.
exposition_filter: Character vector of exposition classes to include; `NULL` for no filter.
reactivity_filter: Character vector of reactivity classes to include; `NULL` for no filter.
return: What to return: `"total"` (default), `"per_locus"`, or `"pairwise"`.
pairwise_locus: When `return = "pairwise"`, the single locus to compute (e.g., `"B"`). Ignored otherwise.

Value

- If `return="total"`: integer total donor-specific eplet load. - If `return="per_locus"`: `data.frame` with columns `locus`, `eplet_load`. - If `return="pairwise"`: numeric matrix where entry `[i,j]` is the count of donor-specific eplets for donor allele `j` vs recipient allele `i` at `pairwise_locus`.

Examples

# Dummy genotypes
recipient <- data.frame(
  A_1 = "A*01:01", A_2 = "A*02:01",
  B_1 = "B*07:02", B_2 = "B*08:01"
)
donor <- data.frame(
  A_1 = "A*03:01", A_2 = "A*24:02",
  B_1 = "B*44:02", B_2 = "B*51:01"
)
rgeno <- hlaGeno(recipient); dgeno <- hlaGeno(donor)

# Total donor-specific eplet load (A1/A2 evidence)
calculateEpletLoad(rgeno, dgeno)
#> [1] 10

# Per locus
calculateEpletLoad(rgeno, dgeno, return = "per_locus")
#>   locus eplet_load
#> 1     A          4
#> 2     B          6

# Pairwise matrix for B locus (rows=recipient alleles, cols=donor alleles)
mB <- calculateEpletLoad(rgeno, dgeno, return = "pairwise", pairwise_locus = "B")
mB
#>          donor
#> recipient B*44:02 B*51:01
#>   B*07:02       5       4
#>   B*08:01       4       3

# Apply additional filters
calculateEpletLoad(rgeno, dgeno, exposition_filter = "High")
#> [1] 8
calculateEpletLoad(rgeno, dgeno, reactivity_filter = c("IgG"))
#> [1] 0