Dev

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 0.2.0
-Date: 2025-06-06 21:26:53 UTC
-SHA: c390a4e79f8ddb3662434d8d4b0e392823443bde
+Version: 0.3.0
+Date: 2025-06-18 18:26:10 UTC
+SHA: 60df41e16cdb635e51b16ff67f857af50e11e0b2

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: immunogenetr
 Title: A Comprehensive Toolkit for Clinical HLA Informatics
-Version: 0.3.0
+Version: 0.3.1
 Authors@R: c(
     person("Nicholas", "Brown", , "nicholas.brown@pennmedicine.upenn.edu", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0002-0046-2315")),

NEWS.md

@@ -1,3 +1,7 @@
+# immunogenetr 0.3.1
+
+* Updated `HLA_columns_to_GLstring` to fix issues processing DRB3/4/5 alleles. 
+
 # immunogenetr 0.3.0
 
 * Updated `ambiguity_table_to_GLstring` to remove duplicate entries from an ambiguity table as it is being processed to a GL string. Added this functionality to `HLA_truncate` so that truncated GL strings could optionally remove duplicates. Added `GLstring_to_ambiguity_table` as an alias for `GL_string_expand_longer`. 

R/HLA_columns_to_GLstring.R

@@ -97,10 +97,20 @@ HLA_columns_to_GLstring <- function(data, HLA_typing_columns, prefix_to_remove =
     # Remove prefixes and suffixes from column names
     mutate(
       truncated_names = str_replace(names, prefix_regex, ""),
-      truncated_names = str_replace(truncated_names, suffix_regex, "")
+      truncated_names = str_replace(truncated_names, suffix_regex, ""),
+      truncated_names = HLA_prefix_remove(truncated_names, keep_locus = TRUE)
     ) %>%
     # Use the HLA_validate function to clean up the typing
     mutate(allele = HLA_validate(allele)) %>%
+    mutate(
+      DRB_locus_raw = case_when(
+        # When the allele starts with “DRB3*”, “DRB4*” or “DRB5*”
+        str_detect(allele, regex("DRB[345]\\*", ignore_case = TRUE)) ~ str_c("HLA-DRB", str_extract(allele, "(?<=DRB)[345]")),
+        # When the allele does not have a "DRB" prefix, instead only has a number prefix
+        str_detect(allele, regex("^[345]\\*", ignore_case = TRUE)) ~ str_c("HLA-DRB", str_extract(allele, "^[345]")),
+        TRUE ~ NA_character_
+      )
+    ) %>%
     # Remove any prefixes in alleles
     mutate(allele = HLA_prefix_remove(allele)) %>%
     # Determine locus name using extended logic
@@ -111,6 +121,7 @@ HLA_columns_to_GLstring <- function(data, HLA_typing_columns, prefix_to_remove =
       str_detect(truncated_names, regex("^Cw[:digit:]?\\*?", ignore_case = TRUE)) ~ "HLA-Cw", # Handle Cw locus
       str_detect(truncated_names, regex("^C[:digit:]?\\*?", ignore_case = TRUE)) ~ "HLA-C", # Handle C locus
       str_detect(truncated_names, regex("^DRB1[:digit:]?\\*?", ignore_case = TRUE)) ~ "HLA-DRB1", # Handle molecular DRB1 locus
+      str_detect(truncated_names, regex("^DRB345", ignore_case = TRUE)) ~ "HLA-DRB345", # Handle column with molecular DRB3/4/5 loci
       str_detect(truncated_names, regex("^DRB3[:digit:]?\\*?", ignore_case = TRUE)) ~ "HLA-DRB3", # Handle molecular DRB3 locus
       str_detect(truncated_names, regex("^DRB4[:digit:]?\\*?", ignore_case = TRUE)) ~ "HLA-DRB4", # Handle molecular DRB4 locus
       str_detect(truncated_names, regex("^DRB5[:digit:]?\\*?", ignore_case = TRUE)) ~ "HLA-DRB5", # Handle molecular DRB5 locus
@@ -138,11 +149,7 @@ HLA_columns_to_GLstring <- function(data, HLA_typing_columns, prefix_to_remove =
     # Determine if the DR typing is one of the DR51/52/53 loci
     mutate(DRB345 = if_else(str_detect(allele, "^5") & locus_from_name == "HLA-DR", TRUE, FALSE)) %>%
     # Handle the final locus name for high-resolution DRB alleles
-    mutate(DRB_locus = if_else(
-      str_detect(locus_from_name, "DRB"), str_c("HLA-DRB", str_extract(allele, "[1345](?=\\*)")), NA_character_
-    )) %>%
-    # Determine the final molecular locus name
-    mutate(molecular_locus = coalesce(DRB_locus, locus_from_name)) %>%
+    mutate(molecular_locus = coalesce(DRB_locus_raw, locus_from_name)) %>%
     # Record "XX" if there is no typing at any of the selected loci.
     mutate(allele = if (all(is.na(allele))) "XX" else allele, .by = c(row_for_function, molecular_locus)) %>%
     # Remove any blank values
@@ -159,7 +166,7 @@ HLA_columns_to_GLstring <- function(data, HLA_typing_columns, prefix_to_remove =
 
   if (nrow(error_table) != 0) {
     # Print the columns that caused the error to assist in debugging
-    abort(format_error(glue::glue("The column(s) {paste(error_column_names, collapse = ', ')} could not be parsed to determine HLA loci.")))
+    rlang::abort(cli::format_error(glue::glue("The column(s) {paste(error_column_names, collapse = ', ')} could not be parsed to determine HLA loci.")))
   }
 
   # Assemble the final type
@@ -170,7 +177,7 @@ HLA_columns_to_GLstring <- function(data, HLA_typing_columns, prefix_to_remove =
       str_glue("{serologic_name}{allele}")
     )) %>%
     # Group alleles within the same locus
-    summarise(final_type_2 = str_flatten(final_type, collapse = "+"), .by = c(row_for_function, locus_from_name, DRB345)) %>%
+    summarise(final_type_2 = str_flatten(final_type, collapse = "+"), .by = c(row_for_function, molecular_locus, DRB345)) %>%
     # Assemble GL string with each locus separated by "^"
     summarise(GL_string = str_flatten(final_type_2, collapse = "^"), .by = row_for_function)
 
@@ -181,5 +188,5 @@ HLA_columns_to_GLstring <- function(data, HLA_typing_columns, prefix_to_remove =
 globalVariables(c(
   ".", "truncated_names", "locus_from_name", "DRB_locus",
   "row_for_function", "molecular_locus", "molecular",
-  "final_type", "DRB345", "final_type_2", "GL_string"
+  "final_type", "DRB345", "final_type_2", "GL_string", "DRB_locus_raw"
 ))

cran-comments.md

@@ -2,5 +2,4 @@
 
 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
 
-* Updated `ambiguity_table_to_GLstring` to remove duplicate entries from an ambiguity table as it is being processed to a GL string. Added this functionality to `HLA_truncate` so that truncated GL strings could optionally remove duplicates. Added `GLstring_to_ambiguity_table` as an alias for `GL_string_expand_longer`. 
-
+* Updated `HLA_columns_to_GLstring` to fix issues processing DRB3/4/5 alleles. 

tests/testthat/test-HLA_columns_to_GLstring.R

@@ -24,4 +24,101 @@ test_that("HLA_columns_to_GLstring correctly converts HLA columns into a GL stri
   expect_true("HLA-A*01:01+HLA-A*11:01^HLA-B*07:02+HLA-B*44:02^HLA-C*03:04+HLA-C*07:01" %in% result)
   expect_true("HLA-A*02:01^HLA-B*08:01+HLA-B*40:01^HLA-C*04:01+HLA-C*07:02" %in% result)
   expect_true("HLA-A*03:01+HLA-A*26:01^HLA-B*15:01^HLA-C*05:01+HLA-C*08:01" %in% result)
+
+  test_1 <- HLA_columns_to_GLstring(HLA_typing_1, c(A1:DPB1_2))
+  result_1 <- c("HLA-A*24:02+HLA-A*29:02^HLA-C*07:04+HLA-C*16:01^HLA-B*44:02+HLA-B*44:03^HLA-DRB5*01:01+HLA-DRB5*01:01^HLA-DRB1*15:01+HLA-DRB1*15:01^HLA-DQA1*01:02+HLA-DQA1*01:02^HLA-DQB1*06:02+HLA-DQB1*06:02^HLA-DPA1*01:03+HLA-DPA1*01:03^HLA-DPB1*03:01+HLA-DPB1*04:01", "HLA-A*02:01+HLA-A*11:05^HLA-C*07:01+HLA-C*07:02^HLA-B*07:02+HLA-B*08:01^HLA-DRB3*01:01^HLA-DRB4*01:03^HLA-DRB1*03:01+HLA-DRB1*04:01^HLA-DQA1*03:03+HLA-DQA1*05:01^HLA-DQB1*02:01+HLA-DQB1*03:01^HLA-DPA1*01:03+HLA-DPA1*01:03^HLA-DPB1*04:01+HLA-DPB1*04:01", "HLA-A*02:01+HLA-A*26:18^HLA-C*02:02+HLA-C*03:04^HLA-B*27:05+HLA-B*54:01^HLA-DRB3*02:02^HLA-DRB4*01:03^HLA-DRB1*04:04+HLA-DRB1*14:54^HLA-DQA1*01:04+HLA-DQA1*03:01^HLA-DQB1*03:02+HLA-DQB1*05:02^HLA-DPA1*01:03+HLA-DPA1*02:02^HLA-DPB1*02:01+HLA-DPB1*05:01", "HLA-A*29:02+HLA-A*30:02^HLA-C*06:02+HLA-C*07:01^HLA-B*08:01+HLA-B*13:02^HLA-DRB4*01:03+HLA-DRB4*01:03^HLA-DRB1*04:01+HLA-DRB1*07:01^HLA-DQA1*02:01+HLA-DQA1*03:01^HLA-DQB1*02:02+HLA-DQB1*03:02^HLA-DPA1*01:03+HLA-DPA1*02:01^HLA-DPB1*01:01+HLA-DPB1*16:01", "HLA-A*02:05+HLA-A*24:02^HLA-C*07:18+HLA-C*12:03^HLA-B*35:03+HLA-B*58:01^HLA-DRB3*02:02+HLA-DRB3*02:02^HLA-DRB1*03:01+HLA-DRB1*14:54^HLA-DQA1*01:04+HLA-DQA1*05:01^HLA-DQB1*02:01+HLA-DQB1*05:03^HLA-DPA1*01:03+HLA-DPA1*02:01^HLA-DPB1*10:01+HLA-DPB1*124:01", "HLA-A*01:01+HLA-A*24:02^HLA-C*07:01+HLA-C*14:02^HLA-B*49:01+HLA-B*51:01^HLA-DRB3*03:01^HLA-DRB1*08:01+HLA-DRB1*13:02^HLA-DQA1*01:02+HLA-DQA1*04:01^HLA-DQB1*04:02+HLA-DQB1*06:04^HLA-DPA1*01:03+HLA-DPA1*01:04^HLA-DPB1*04:01+HLA-DPB1*15:01", "HLA-A*03:01+HLA-A*03:01^HLA-C*03:03+HLA-C*16:01^HLA-B*15:01+HLA-B*51:01^HLA-DRB4*01:01^HLA-DRB1*01:01+HLA-DRB1*07:01^HLA-DQA1*01:01+HLA-DQA1*02:01^HLA-DQB1*02:02+HLA-DQB1*05:01^HLA-DPA1*01:03+HLA-DPA1*01:03^HLA-DPB1*04:01+HLA-DPB1*04:01", "HLA-A*01:01+HLA-A*32:01^HLA-C*06:02+HLA-C*07:02^HLA-B*08:01+HLA-B*37:01^HLA-DRB3*02:02^HLA-DRB5*01:01^HLA-DRB1*03:01+HLA-DRB1*15:01^HLA-DQA1*01:02+HLA-DQA1*05:01^HLA-DQB1*02:01+HLA-DQB1*06:02^HLA-DPA1*01:03+HLA-DPA1*02:01^HLA-DPB1*04:01+HLA-DPB1*14:01", "HLA-A*03:01+HLA-A*30:01^HLA-C*07:02+HLA-C*12:03^HLA-B*07:02+HLA-B*38:01^HLA-DRB3*01:01^HLA-DRB5*01:01^HLA-DRB1*03:01+HLA-DRB1*15:01^HLA-DQA1*01:02+HLA-DQA1*05:01^HLA-DQB1*02:01+HLA-DQB1*06:02^HLA-DPA1*01:03+HLA-DPA1*01:03^HLA-DPB1*04:01+HLA-DPB1*04:01", "HLA-A*02:05+HLA-A*11:01^HLA-C*07:18+HLA-C*16:02^HLA-B*51:01+HLA-B*58:01^HLA-DRB3*03:01^HLA-DRB5*01:01^HLA-DRB1*13:02+HLA-DRB1*15:01^HLA-DQA1*01:02+HLA-DQA1*01:03^HLA-DQB1*06:01+HLA-DQB1*06:09^HLA-DPA1*01:03+HLA-DPA1*01:03^HLA-DPB1*02:01+HLA-DPB1*104:01")
+  expect_equal(test_1, result_1)
+
+  test_LIS <- HLA_columns_to_GLstring(HLA_typing_LIS, c(mA1Cd.recipient:mDPB12cd.recipient), prefix_to_remove = "m", suffix_to_remove = "cd.recipient")
+  result_LIS <- c("HLA-A*24:02+HLA-A*02:01^HLA-B*40:02+HLA-B*40:01^HLA-C*03:04^HLA-DRB1*10:01+HLA-DRB1*15:01^HLA-DRB5*01:01^HLA-DQA1*01:05+HLA-DQA1*01:02^HLA-DQB1*05:01+HLA-DQB1*06:02^HLA-DPA1*01:03^HLA-DPB1*02:01+HLA-DPB1*04:01", "HLA-A*03:01+HLA-A*74:01^HLA-B*53:01+HLA-B*57:03^HLA-C*04:01+HLA-C*07:01^HLA-DRB1*11:01+HLA-DRB1*16:02^HLA-DRB3*02:02^HLA-DRB5*02:21^HLA-DQA1*01:02+HLA-DQA1*05:05^HLA-DQB1*03:19+HLA-DQB1*05:02^HLA-DPA1*02:01+HLA-DPA1*02:02^HLA-DPB1*01:01", "HLA-A*11:01+HLA-A*32:01^HLA-B*52:01^HLA-C*12:02^HLA-DRB1*15:02^HLA-DRB5*01:02^HLA-DQA1*01:03^HLA-DQB1*06:01^HLA-DPA1*01:03+HLA-DPA1*02:07^HLA-DPB1*02:01+HLA-DPB1*04:01", "HLA-A*03:01+HLA-A*30:02^HLA-B*14:02^HLA-C*08:02^HLA-DRB1*01:02+HLA-DRB1*13:02^HLA-DRB3*03:01^HLA-DQA1*01:01+HLA-DQA1*01:02^HLA-DQB1*05:01+HLA-DQB1*06:09^HLA-DPA1*02:01^HLA-DPB1*05:01+HLA-DPB1*17:01", "HLA-A*01:01+HLA-A*24:02^HLA-B*07:02^HLA-C*07:02^HLA-DRB1*01:01+HLA-DRB1*15:01^HLA-DRB5*01:01^HLA-DQA1*01:01+HLA-DQA1*01:02^HLA-DQB1*05:01+HLA-DQB1*06:02^HLA-DPA1*01:03+HLA-DPA1*02:01^HLA-DPB1*04:01+HLA-DPB1*11:01", "HLA-A*02:01+HLA-A*30:02^HLA-B*39:11+HLA-B*41:01^HLA-C*07:02+HLA-C*17:01^HLA-DRB1*03:01+HLA-DRB1*04:05^HLA-DRB3*02:02^HLA-DRB4*01:03^HLA-DQA1*05:01+HLA-DQA1*03:03^HLA-DQB1*02:01+HLA-DQB1*02:02^HLA-DPA1*01:03^HLA-DPB1*02:01+HLA-DPB1*04:01", "HLA-A*02:17+HLA-A*32:01^HLA-B*40:02^HLA-C*02:02+HLA-C*03:05^HLA-DRB1*04:11+HLA-DRB1*13:01^HLA-DRB3*02:02^HLA-DRB4*01:03^HLA-DQA1*03:01+HLA-DQA1*01:03^HLA-DQB1*03:02+HLA-DQB1*06:03^HLA-DPA1*01:03^HLA-DPB1*04:02", "HLA-A*11:01+HLA-A*23:01^HLA-B*15:17+HLA-B*44:03^HLA-C*07:01+HLA-C*16:01^HLA-DRB1*07:01^HLA-DRB4*01:01+HLA-DRB4*01:03^HLA-DQA1*02:01^HLA-DQB1*02:02^HLA-DPA1*01:03+HLA-DPA1*02:01^HLA-DPB1*04:01+HLA-DPB1*11:01", "HLA-A*03:01+HLA-A*68:02^HLA-B*08:01+HLA-B*15:03^HLA-C*02:10+HLA-C*03:04^HLA-DRB1*13:04+HLA-DRB1*07:01^HLA-DRB3*02:02^HLA-DRB4*01:03^HLA-DQA1*02:01+HLA-DQA1*05:05^HLA-DQB1*02:02+HLA-DQB1*03:19^HLA-DPA1*01:03+HLA-DPA1*02:02^HLA-DPB1*01:01+HLA-DPB1*02:01", "HLA-A*01:01+HLA-A*02:01^HLA-B*08:01+HLA-B*07:02^HLA-C*07:01+HLA-C*05:01^HLA-DRB1*03:01+HLA-DRB1*04:01^HLA-DRB3*01:01^HLA-DRB4*01:03^HLA-DQA1*05:01+HLA-DQA1*03:03^HLA-DQB1*02:01+HLA-DQB1*03:01^HLA-DPA1*01:03^HLA-DPB1*04:01+HLA-DPB1*06:01")
+  expect_equal(test_LIS, result_LIS)
+
+  test_freq <- HLA_columns_to_GLstring(Haplotype_frequencies, c("HLA-A":"HLA-DPB1"))
+  result_freq <- c("HLA-A*24:02:01:01^HLA-C*03:04:01:01^HLA-B*40:01:02^HLA-DRB1*08:01:01^HLA-DQA1*04:01:01^HLA-DQB1*04:02:01^HLA-DPA1*01:03:01:04^HLA-DPB1*04:01:01:01", "HLA-A*03:01:01:05^HLA-C*06:02:01:01^HLA-B*47:01:01:03^HLA-DRB4*01:01:01:01^HLA-DRB1*07:01:01:01^HLA-DQA1*02:01:01:01^HLA-DQB1*02:02:01:01^HLA-DPA1*01:03:01:03^HLA-DPB1*06:01:01", "HLA-A*02:01:01:01^HLA-C*05:01:01:02^HLA-B*44:02:01:01^HLA-DRB3*01:01:02:01^HLA-DRB1*03:01:01:01^HLA-DQA1*05:01:01:02^HLA-DQB1*02:01:01^HLA-DPA1*01:03:01:01^HLA-DPB1*02:01:02", "HLA-A*32:01:01^HLA-C*02:02:02:01^HLA-B*40:02:01^HLA-DRB3*02:02:01:02^HLA-DRB1*11:01:01:01^HLA-DQA1*05:05:01:01^HLA-DQB1*03:01:01:03^HLA-DPA1*01:03:01:01^HLA-DPB1*02:01:02", "HLA-A*02:01:01:01^HLA-C*05:01:01:02^HLA-B*44:02:01:01^HLA-DRB5*01:01:01^HLA-DRB1*15:01:01:01^HLA-DQA1*01:02:01:01^HLA-DQB1*06:02:01^HLA-DPA1*01:03:01:02^HLA-DPB1*04:01:01:01", "HLA-A*02:01:01:01^HLA-C*05:01:01:02^HLA-B*44:02:01:01^HLA-DRB4*01:03:01:01^HLA-DRB1*04:01:01:01^HLA-DQA1*03:03:01:01^HLA-DQB1*03:01:01:01^HLA-DPA1*01:03:01:05^HLA-DPB1*04:02:01:02", "HLA-A*02:06:01:01^HLA-C*08:01:01^HLA-B*40:06:01:01^HLA-DRB4*01:03:02^HLA-DRB1*09:01:02^HLA-DQA1*03:02^HLA-DQB1*03:03:02:02^HLA-DPA1*02:01:01:02^HLA-DPB1*09:01:01", "HLA-A*24:02:01:01^HLA-C*07:02:01:01^HLA-B*39:05:01^HLA-DRB5*02:02^HLA-DRB1*16:02:01:02^HLA-DQA1*05:05:01:05^HLA-DQB1*03:01:01:01^HLA-DPA1*01:03:01:05^HLA-DPB1*04:02:01:02", "HLA-A*02:01:01:01^HLA-C*02:02:02:01^HLA-B*40:02:01^HLA-DRB3*02:02:01:02^HLA-DRB1*13:01:01:01^HLA-DQA1*01:03:01:02^HLA-DQB1*06:03:01^HLA-DPA1*01:03:01:01^HLA-DPB1*02:01:02", "HLA-A*24:02:01:01^HLA-C*07:04:01:01^HLA-B*44:02:01:03^HLA-DRB3*02:02:01:02^HLA-DRB1*11:01:01:01^HLA-DQA1*05:05:01:01^HLA-DQB1*03:01:01:03^HLA-DPA1*01:03:01:01^HLA-DPB1*02:01:02")
+  expect_equal(test_freq, result_freq)
+
+
+  test_separate_DRB_no_prefixes <- tibble(
+    patient = c("patient1", "patient2", "patient3"),
+    DRB3_1  = c("03:01", NA, "03:03"),
+    DRB4_1  = c(NA, "04:02", NA),
+    DRB5_1  = c(NA, NA, "05:03")
+  )
+  result_separate_no_prefixes <- test_separate_DRB_no_prefixes %>%
+    mutate(GL = HLA_columns_to_GLstring(., HLA_typing_columns = DRB3_1:DRB5_1)) %>%
+    pull(GL)
+  expect_equal(
+    result_separate_no_prefixes,
+    c("HLA-DRB3*03:01", "HLA-DRB4*04:02", "HLA-DRB3*03:03^HLA-DRB5*05:03")
+  )
+
+  test_separate_DRB_numeric_only <- tibble(
+    patient = c("patient1", "patient2", "patient3"),
+    DRB3_1  = c("3*03:01", NA, "3*03:03"),
+    DRB4_1  = c(NA, "4*04:02", NA),
+    DRB5_1  = c(NA, NA, "5*05:03")
+  )
+  result_separate_numeric_only <- test_separate_DRB_numeric_only %>%
+    mutate(GL = HLA_columns_to_GLstring(., HLA_typing_columns = DRB3_1:DRB5_1)) %>%
+    pull(GL)
+  expect_equal(
+    result_separate_numeric_only,
+    c("HLA-DRB3*03:01", "HLA-DRB4*04:02", "HLA-DRB3*03:03^HLA-DRB5*05:03")
+  )
+
+  test_separate_DRB_full_prefix <- tibble(
+    patient = c("patient1", "patient2", "patient3"),
+    DRB3_1  = c("DRB3*03:01", NA, "DRB3*03:03"),
+    DRB4_1  = c(NA, "DRB4*04:02", NA),
+    DRB5_1  = c(NA, NA, "DRB5*05:03")
+  )
+  result_separate_full_prefix <- test_separate_DRB_full_prefix %>%
+    mutate(GL = HLA_columns_to_GLstring(., HLA_typing_columns = DRB3_1:DRB5_1)) %>%
+    pull(GL)
+  expect_equal(
+    result_separate_full_prefix,
+    c("HLA-DRB3*03:01", "HLA-DRB4*04:02", "HLA-DRB3*03:03^HLA-DRB5*05:03")
+  )
+
+  test_mixed_DRB_with_prefixes <- tibble(
+    patient = c("patient1", "patient2", "patient3"),
+    DRB345_1 = c("DRB3*01:01", "DRB4*04:01", "DRB5*05:01"),
+    DRB345_2 = c("DRB4*01:01", "DRB5*04:01", "DRB5*05:02")
+  )
+  result_mixed_with_prefixes <- test_mixed_DRB_with_prefixes %>%
+    mutate(GL = HLA_columns_to_GLstring(., HLA_typing_columns = DRB345_1:DRB345_2)) %>%
+    pull(GL)
+  expect_equal(
+    result_mixed_with_prefixes,
+    c(
+      "HLA-DRB3*01:01^HLA-DRB4*01:01", "HLA-DRB4*04:01^HLA-DRB5*04:01",
+      "HLA-DRB5*05:01+HLA-DRB5*05:02"
+    )
+  )
+
+  test_mixed_DRB_no_prefixes <- tibble(
+    patient = c("patient1", "patient2", "patient3"),
+    DRB345_1 = c("3*01:01", "4*04:01", "5*05:01")
+  )
+  result_mixed_no_prefixes <- test_mixed_DRB_no_prefixes %>%
+    mutate(GL = HLA_columns_to_GLstring(., HLA_typing_columns = DRB345_1)) %>%
+    pull(GL)
+  expect_equal(
+    result_mixed_no_prefixes,
+    c("HLA-DRB3*01:01", "HLA-DRB4*04:01", "HLA-DRB5*05:01")
+  )
+
+  test_sero <- tibble(
+    patient = c("patient1", "patient2", "patient3"),
+    A_1 = c("2", "3", "68"),
+    A_2 = c("", "1", "69"),
+    DR_1 = c("7", 4, "9"),
+    DR_2 = c("6", "4", NA),
+    DRw_1 = c(NA, NA, "52"),
+    DRw_2 = c("51", "52", "53")
+  )
+
+  test_sero_code <- test_sero %>% HLA_columns_to_GLstring(HLA_typing_columns = A_1:DRw_2)
+  test_sero_result <- c("HLA-A2^HLA-DR7+HLA-DR6^HLA-DR51", "HLA-A3+HLA-A1^HLA-DR4+HLA-DR4^HLA-DR52", "HLA-A68+HLA-A69^HLA-DR9^HLA-DR52+HLA-DR53")
+  expect_equal(test_sero_code, test_sero_result)
 })