tests/testthat/test-HLA_match_number.R

In immunogenetr: A Comprehensive Toolkit for Clinical HLA Informatics

library(testthat)
library(dplyr)
library(stringr)

test_that("HLA_match_number correctly calculates HLA match numbers across different scenarios", {
  GL_string_recip <- "HLA-A*01:01+HLA-A*02:01^HLA-B*07:02+HLA-B*08:01^HLA-DRB1*04:01+HLA-DRB1*07:01"
  GL_string_donor <- "HLA-A*01:01+HLA-A*03:01^HLA-B*07:02+HLA-B*44:02^HLA-DRB1*04:01+HLA-DRB1*13:01"
  loci <- c("HLA-A", "HLA-B", "HLA-DRB1")

  result_HvG <- HLA_match_number(GL_string_recip, GL_string_donor, loci, direction = "HvG")
  result_GvH <- HLA_match_number(GL_string_recip, GL_string_donor, loci, direction = "GvH")
  result_bidirectional <- HLA_match_number(GL_string_recip, GL_string_donor, loci, direction = "bidirectional")

  expect_match(result_HvG, "HLA-A=1, HLA-B=1, HLA-DRB1=1")
  expect_match(result_GvH, "HLA-A=1, HLA-B=1, HLA-DRB1=1")
  expect_match(result_bidirectional, "HLA-A=1, HLA-B=1, HLA-DRB1=1")

  perfect_match <- HLA_match_number(GL_string_recip, GL_string_recip, loci, direction = "bidirectional")
  expect_match(perfect_match, "HLA-A=2, HLA-B=2, HLA-DRB1=2")

  GL_string_mismatch <- "HLA-A*24:01+HLA-A*25:01^HLA-B*51:01+HLA-B*52:01^HLA-DRB1*15:01+HLA-DRB1*16:01"
  mismatch_result <- HLA_match_number(GL_string_recip, GL_string_mismatch, loci, direction = "bidirectional")
  expect_match(mismatch_result, "HLA-A=0, HLA-B=0, HLA-DRB1=0")

  result_A <- HLA_match_number(GL_string_recip, GL_string_donor, "HLA-A", direction = "HvG")
  result_B <- HLA_match_number(GL_string_recip, GL_string_donor, "HLA-B", direction = "HvG")
  result_DRB1 <- HLA_match_number(GL_string_recip, GL_string_donor, "HLA-DRB1", direction = "HvG")

  expect_equal(result_A, 1)
  expect_equal(result_B, 1)
  expect_equal(result_DRB1, 1)

  expect_error(HLA_match_number(GL_string_recip, GL_string_donor, loci, direction = "invalid"))
})