hlaToVariable {midasHLA} | R Documentation

## 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")

[Package midasHLA version 1.2.0 Index]