HLAGene_: R6 Class '"HLAGene"'

In gschofl/hlatools: A collection of tools to work with IPD-IMGT/HLA data

Description

R6 Class "HLAGene"

R6 Class "HLAGene"

Details

A container for the allelic information of an HLA gene.

Methods

Public methods

• HLAGene_$new()

• HLAGene_$print()

• HLAGene_$get_hlatools_version()

• HLAGene_$get_db_version()

• HLAGene_$get_locusname()

• HLAGene_$get_alleles()

• HLAGene_$has_distances()

• HLAGene_$calculate_exon_distance_matrix()

• HLAGene_$get_closest_complete_neighbor()

• HLAGene_$get_reference_sequence()

• HLAGene_$get_all_reference_sequences()

• HLAGene_$get_reference_sequence_as_ft()

• HLAGene_$get_all_reference_sequences_as_ft()

• HLAGene_$get_extended_reference_set()

• HLAGene_$clone()

---

Method new()

Create a new HLAgene object.

Usage

HLAGene_$new(
  locusname,
  db_version,
  db_path = getOption("hlatools.local_repos"),
  ncores = parallel::detectCores() - 2,
  with_dist = FALSE
)

Arguments

locusname

Name of locus.

db_version

Version number of IPD-IMGT/HLA release or "Latest".

db_path

Local path to IPD-IMGT/HLA.

ncores

How many cores are used for parsing the data.

with_dist

Calulate Levenshtein distances between all alleles.

Returns

A new HLAgene object.

---

Method print()

Display a HLAgene object.

Usage

HLAGene_$print()

---

Method get_hlatools_version()

The package version under which a HLAGene object was created.

Usage

HLAGene_$get_hlatools_version()

---

Method get_db_version()

The IPD-IMGT/HLA database version.

Usage

HLAGene_$get_db_version()

---

Method get_locusname()

The name of the HLA locus.

Usage

HLAGene_$get_locusname()

---

Method get_alleles()

A HLAAllele object.

Usage

HLAGene_$get_alleles(allele)

Arguments

allele

The allele code.

---

Method has_distances()

Has a distance matrix between all alleles been calculated?

Usage

HLAGene_$has_distances()

---

Method calculate_exon_distance_matrix()

Calculate a distance matrix between all alleles based on the available exon sequences.

Usage

HLAGene_$calculate_exon_distance_matrix()

---

Method get_closest_complete_neighbor()

Get the full-length allele that is closest to the query allele, based on the available exon sequences.

Usage

HLAGene_$get_closest_complete_neighbor(allele, partially = TRUE)

Arguments

allele

The allele code.

partially

If TRUE match partial allele names.

---

Method get_reference_sequence()

Get the reference sequence for query allele extended to full length by filling up missing sequence information with the closest complete neighbour.

Usage

HLAGene_$get_reference_sequence(allele)

Arguments

allele

The allele code.

---

Method get_all_reference_sequences()

Get the reference sequences for all allele extended to full length by filling up missing sequence information with the closest complete neighbours.

Usage

HLAGene_$get_all_reference_sequences(allele)

Arguments

allele

The allele code.

---

Method get_reference_sequence_as_ft()

Get the reference sequence for query allele extended to full length by filling up missing sequence information with the closest complete neighbour formatted as a GenBank Feature Table.

Usage

HLAGene_$get_reference_sequence_as_ft(allele)

Arguments

allele

The allele code.

---

Method get_all_reference_sequences_as_ft()

Get the reference sequences for all allele extended to full length by filling up missing sequence information with the closest complete neighbours formatted as a GenBank Feature Table.

Usage

HLAGene_$get_all_reference_sequences_as_ft(allele)

Arguments

allele

The allele code.

---

Method get_extended_reference_set()

TODO: Documentation

Usage

HLAGene_$get_extended_reference_set(verbose = FALSE)

Arguments

verbose

Emit progress messages.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

HLAGene_$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

gschofl/hlatools documentation built on July 2, 2021, 10:59 a.m.