immunogenetr

install.packages("immunogenetr")

library(immunogenetr)
library(tidyverse)

# The "HLA_typing_1" dataset is installed with immunogenetr, and contains high resolution typing at all classical 
# HLA loci for ten individuals.

print(HLA_typing_1)

HLA_typing_1_GLstring <- HLA_typing_1 %>% 
  mutate(GL_string = HLA_columns_to_GLstring(., HLA_typing_columns = A1:DPB1_2), .after = patient) %>% 
  # Note the syntax for the `HLA_columns_to_GLstring` arguments - when this function is used inside 
  # of a `mutate` function to make a new column in a data frame, "." is used in the first argument 
  # to tell the function to use the working data frame as the source of the HLA typing columns.
  select(patient, GL_string)

print(HLA_typing_1_GLstring)

# Select one case each for recipient and donor.
HLA_typing_1_GLstring_recipient <- HLA_typing_1_GLstring %>% 
  filter(patient == 7) %>% 
  rename(GL_string_recipient = GL_string, case = patient)

HLA_typing_1_GLstring_donor <- HLA_typing_1_GLstring %>% 
  filter(patient == 9) %>% 
  rename(GL_string_donor = GL_string) %>% 
  select(-patient)

# Combine the tables so recipient and donor are on the same row.
HLA_typing_1_recip_donor <- bind_cols(
  HLA_typing_1_GLstring_recipient, 
  HLA_typing_1_GLstring_donor
  )

print(HLA_typing_1_recip_donor)

HLA_typing_1_recip_donor_mismatches <- HLA_typing_1_recip_donor %>% 
  mutate(A_MM_GvH = HLA_mismatch_logical(
                      GL_string_recipient, 
                      GL_string_donor, 
                      "HLA-A", 
                      direction = "GvH"), 
                    .after = case) %>% 
  mutate(A_MM_HvG = HLA_mismatch_logical(
                      GL_string_recipient, 
                      GL_string_donor, 
                      "HLA-A", 
                      direction = "HvG"), 
                    .after = A_MM_GvH)

print(HLA_typing_1_recip_donor_mismatches)

HLA_typing_1_recip_donor_mismatched_allles <- HLA_typing_1_recip_donor %>% 
  mutate(A_HvG_MMs = HLA_mismatched_alleles(
                        GL_string_recipient, 
                        GL_string_donor, 
                        "HLA-A", 
                        direction = "HvG"), 
                      .after = case)

print(HLA_typing_1_recip_donor_mismatched_allles)

# Determine the number of bidirectional mismatches at several loci.
HLA_typing_1_recip_donor_MM_number <- HLA_typing_1_recip_donor %>% 
  mutate(ABCDRB1_MM = HLA_mismatch_number(
                        GL_string_recipient, 
                        GL_string_donor, 
                        c("HLA-A", "HLA-B", "HLA-C", "HLA-DRB1"), 
                        direction = "bidirectional"), 
                      .after = case)

print(HLA_typing_1_recip_donor_MM_number)

# The match_grade argument of "Xof8" will return the number of matches at the HLA-A, B, C, and DRB1 loci.
HLA_typing_1_recip_donor_8of8_matching <- HLA_typing_1_recip_donor %>% 
  mutate(ABCDRB1_matching = HLA_match_summary_HCT(
                              GL_string_recipient, 
                              GL_string_donor, 
                              direction = "bidirectional", 
                              match_grade = "Xof8"), 
                            .after = case)

print(HLA_typing_1_recip_donor_8of8_matching)

# Select one case to be the recipient.
HLA_typing_1_GLstring_candidate <- HLA_typing_1_GLstring %>% 
  filter(patient == 3) %>% 
  select(GL_string) %>% 
  rename(GL_string_recip = GL_string)

# Join the recipient to the 10-donor list and perform matching
HLA_typing_1_GLstring_donors <- HLA_typing_1_GLstring %>% 
  rename(GL_string_donor = GL_string, donor = patient) %>% 
  cross_join(HLA_typing_1_GLstring_candidate) %>%
  mutate(ABCDRB1_matching = HLA_match_summary_HCT(
                              GL_string_recip, 
                              GL_string_donor, 
                              direction = "bidirectional", 
                              match_grade = "Xof8"), 
                            .after = donor) %>%
  arrange(desc(ABCDRB1_matching))

print(HLA_typing_1_GLstring_donors)