immunogenetr (version 0.3.1)

ambiguity_table_to_GLstring: ambiguity_table_to_GLstring

Description

A function that converts a data table of HLA allele ambiguities (e.g. as created by `GLstring_expand_longer` or `GLstring_to_ambiguity_table`) into a GL string format. The function processes the table by combining allele ambiguities, haplotypes, gene copies, and loci into a structured GL string.

Usage

ambiguity_table_to_GLstring(data, remove_duplicates = FALSE)

Value

A GL string representing the combined gene locations, loci, genotype ambiguities, genotypes, and haplotypes.

Arguments

data

A data frame containing columns that represent possible gene locations, loci, genotype ambiguities, genotypes, and haplotypes.

remove_duplicates

A logical value indicating if the function will check for duplicate entries at each step and remove them before assembling the final GL string. Useful if the ambiguity table has been altered, for example by truncating allele designations. Default is FALSE.

Examples

# Example data frame input
data <- tibble::tribble(
  ~value, ~entry, ~possible_gene_location,
  ~locus, ~genotype_ambiguity, ~genotype, ~haplotype, ~allele,
  "HLA-A*01:01:01:01", 1, 1,
  1, 1, 1, 1, 1,
  "HLA-A*01:02", 1, 1,
  1, 1, 1, 1, 2,
  "HLA-A*01:03", 1, 1,
  1, 1, 1, 1, 3,
  "HLA-A*01:95", 1, 1,
  1, 1, 1, 1, 4,
  "HLA-A*24:02:01:01", 1, 1,
  1, 1, 2, 1, 1,
  "HLA-A*01:01:01:01", 1, 1,
  1, 2, 1, 1, 1,
  "HLA-A*01:03", 1, 1,
  1, 2, 1, 1, 2,
  "HLA-A*24:03:01:01", 1, 1,
  1, 2, 2, 1, 1,
  "HLA-B*07:01:01", 1, 1,
  2, 1, 1, 1, 1,
  "B*15:01:01", 1, 1,
  2, 1, 2, 1, 1,
  "B*15:02:01", 1, 1,
  2, 1, 2, 1, 2,
  "B*07:03", 1, 1,
  2, 2, 1, 1, 1,
  "B*15:99:01", 1, 1,
  2, 2, 2, 1, 1,
  "HLA-DRB1*03:01:02", 1, 1,
  3, 1, 1, 1, 1,
  "HLA-DRB5*01:01:01", 1, 1,
  3, 1, 1, 2, 1,
  "HLA-KIR2DL5A*0010101", 1, 1,
  3, 1, 2, 1, 1,
  "HLA-KIR2DL5A*0010201", 1, 1,
  3, 1, 3, 1, 1,
  "HLA-KIR2DL5B*0010201", 1, 2,
  1, 1, 1, 1, 1,
  "HLA-KIR2DL5B*0010301", 1, 2,
  1, 1, 2, 1, 1
)

ambiguity_table_to_GLstring(data)