hlaToVariable: Convert HLA calls to variables

In Genentech/MiDAS: R package for immunogenomics data handling and association analysis

Convert HLA calls to variables

Description

hlaToVariable converts HLA calls data frame to additional variables.

Usage

hlaToVariable(
  hla_calls,
  dictionary,
  reduce = TRUE,
  na.value = 0,
  nacols.rm = TRUE
)

Arguments

hla_calls	HLA calls data frame, as returned by readHlaCalls function.
dictionary	Path to file containing HLA allele dictionary or a data frame.
reduce	Logical indicating if function should try to reduce allele resolution when no matching entry in the dictionary is found. See details.
na.value	Vector of length one speciyfing value for alleles with no matching entry in dictionary. Default is to use 0.
nacols.rm	Logical indicating if result columns that contain only NA should be removed.

Details

dictionary file should be a tsv format with header and two columns. First column should hold allele numbers and second corresponding additional variables. Optionally a data frame formatted in the same manner can be passed instead.

dictionary can be also used to access dictionaries shipped with the package. They can be referred to by using one of the following strings:

"allele_HLA_Bw"

Translates HLA-B alleles together with A*23, A*24 and A*32 into Bw4 and Bw6 allele groups. In some cases HLA alleles containing Bw4 epitope, on nucleotide level actually carries a premature stop codon. Meaning that although on nucleotide level the allele would encode a Bw4 epitope it's not really there and it is assigned to Bw6 group. However in 4-digit resolution these alleles can not be distinguished from other Bw4 groups. Since alleles with premature stop codons are rare, Bw4 group is assigned.

"allele_HLA-B_only_Bw"

Translates HLA-B alleles (without A*23, A*24 and A*32) into Bw4 and Bw6 allele groups.

"allele_HLA-C_C1-2"

Translates HLA-C alleles into C1 and C2 allele groups.

"allele_HLA_supertype"

Translates HLA-A and HLA-B alleles into supertypes, a classification that group HLA alleles based on peptide binding specificities.

"allele_HLA_Ggroup"

Translates HLA alleles into G groups, which defines amino acid identity only in the exons relevant for peptide binding. Note that alleles DRB1*01:01:01 and DRB1*01:16 match more than one G group, here this ambiguity was removed by deleting matching with DRB5*01:01:01G group.

reduce control if conversion should happen in a greedy way, such that if some HLA number cannot be converted, it's resolution is reduced by 2 and another attempt is taken. This process stops when alleles cannot be further reduced or all have been successfully converted.

Value

Data frame with variable number of columns. First column named "ID" corresponds to "ID" column in hla_calls, further columns holds converted HLA variables.

Examples

hlaToVariable(MiDAS_tut_HLA, dictionary = "allele_HLA_supertype")

Genentech/MiDAS documentation built on Feb. 5, 2024, 11:52 a.m.