Package 'immReferent' reference manual

Title:	An Interface for Immune Receptor and HLA Gene Reference Data
Description:	Provides a consistent interface for downloading, storing, and accessing immune receptor (TCR/BCR) and HLA sequences from IMGT, IPD-IMGT/HLA, and OGRDB (AIRR-C). Supports export to popular analysis tools including MiXCR, TRUST4, Cell Ranger, and IgBLAST. This package serves as a core dependency for immunogenomics packages, ensuring reliable and high-quality sequence access with local caching for reproducibility.
Authors:	Nick Borcherding [aut, cre]
Maintainer:	Nick Borcherding <[email protected]>
License:	MIT + file LICENSE
Version:	1.1.0
Built:	2026-05-30 07:53:38 UTC
Source:	https://github.com/bioc/immReferent

immReferent: An Interface for Immune Receptor and HLA Gene Reference Data

Description

immReferent provides a stable, reproducible, and lightweight interface to reference sequences for immune receptors (TCR/BCR) and HLA genes sourced from IMGT, IPD-IMGT/HLA, and the AIRR-C's OGRDB. It centralizes downloading, caching, and querying of curated nucleotide and protein sequences, and plays a foundational role in computational immunology workflows.

Details

The package is designed as a common reference layer across immunoinformatics tools, ensuring consistent provenance and offline reproducibility via caching.

Core functionality

Download and parse receptor and HLA sequences from IMGT and OGRDB
Local caching to support offline, reproducible analysis
Query by gene, allele, species, locus, and sequence type/format
Export to popular analysis tools (MiXCR, TRUST4, Cell Ranger, IgBLAST)
Interoperability with Bioconductor classes such as DNAStringSet and AAStringSet

Data retrieval functions

getIMGT: Download sequences from IMGT
getOGRDB: Download sequences from OGRDB
loadIMGT, loadOGRDB: Load cached sequences
refreshIMGT, refreshOGRDB: Force re-download

Export functions

exportMiXCR: Export for MiXCR analysis
exportTRUST4: Export for TRUST4 analysis
exportCellRanger: Export for 10x Cell Ranger VDJ
exportIgBLAST: Export for IgBLAST analysis

Supported data sources

IMGT: The international ImMunoGeneTics information system (https://www.imgt.org/)
IPD-IMGT/HLA: The HLA Database (https://www.ebi.ac.uk/ipd/imgt/hla/)
OGRDB: Open Germline Receptor Database (AIRR-C) (https://ogrdb.airr-community.org/)

Getting started

browseVignettes("immReferent")

Attribution and Licensing

Data obtained from IMGT and OGRDB must be cited according to their terms. IMGT data are distributed under a CC BY-NC-ND 4.0 license. Proper attribution is required, and derivative or commercial use is restricted per IMGT policy. Always review the current licensing and citation requirements of each resource prior to use.

Author(s)

Maintainer: Nick Borcherding [email protected]

Export Reference Sequences to Cell Ranger VDJ Format

Description

Exports a DNAStringSet to FASTA format suitable for creating a custom Cell Ranger VDJ reference. The function generates a FASTA file with properly formatted headers for use with cellranger mkvdjref.

Usage

exportCellRanger(sequences, output_file, gene_type = NULL)
exportCellRanger(sequences, output_file, gene_type = NULL)

Arguments

sequences

A DNAStringSet object containing immune receptor sequences. Sequence names must follow standard IG/TR gene nomenclature (e.g., "IGHV1-2*01"). Can be obtained from getIMGT or getOGRDB.

output_file

Character string specifying the path to the output FASTA file. The parent directory will be created if it does not exist.

gene_type

Character string specifying the type of gene region. One of "V", "D", "J", or "C". If NULL (default), the function will attempt to infer the type from sequence names.

Details

Cell Ranger's mkvdjref command expects FASTA files with specific header formats. This function creates a FASTA file that can be used as input to build a custom VDJ reference.

Note: For a complete Cell Ranger VDJ reference, you also need a GTF file with gene annotations. This function only creates the FASTA component.

This function works with sequences from both IMGT (via getIMGT) and OGRDB (via getOGRDB).

Value

Character string with the path to the created file, returned invisibly.

Examples

# Create a small example DNAStringSet
seqs <- Biostrings::DNAStringSet(c(
  "ATGCGATCGATCGATCG",
  "ATGCGATCGATCG"
))
names(seqs) <- c("IGHV1-2*01", "IGHV1-3*01")

# Export to temporary file
output_file <- tempfile(fileext = ".fa")
exportCellRanger(seqs, output_file)

# View the result
cat(readLines(output_file), sep = "\n")

# Clean up
unlink(output_file)
# Create a small example DNAStringSet
seqs <- Biostrings::DNAStringSet(c(
  "ATGCGATCGATCGATCG",
  "ATGCGATCGATCG"
))
names(seqs) <- c("IGHV1-2*01", "IGHV1-3*01")

# Export to temporary file
output_file <- tempfile(fileext = ".fa")
exportCellRanger(seqs, output_file)

# View the result
cat(readLines(output_file), sep = "\n")

# Clean up
unlink(output_file)

Export Reference Sequences to IgBLAST Format

Description

Exports a DNAStringSet to FASTA files formatted for use with IgBLAST. The function creates separate FASTA files for V, D, and J gene segments with simplified headers compatible with IgBLAST's requirements.

Usage

exportIgBLAST(
  sequences,
  output_dir,
  organism = "custom",
  receptor_type = c("ig", "tcr")
)
exportIgBLAST(
  sequences,
  output_dir,
  organism = "custom",
  receptor_type = c("ig", "tcr")
)

Arguments

sequences

A DNAStringSet object containing immune receptor sequences. Sequence names must follow standard IG/TR gene nomenclature (e.g., "IGHV1-2*01"). Can be obtained from getIMGT or getOGRDB.

output_dir

Character string specifying the directory where output files will be written. The directory will be created if it does not exist.

organism

Character string specifying the organism name for the output files. Used in file naming. Default is "custom".

receptor_type

Character string specifying the receptor type. One of "ig" for immunoglobulin or "tcr" for T-cell receptor. Default is "ig".

Details

IgBLAST requires FASTA files with simplified headers containing only the gene/allele name. This function mimics the output of IgBLAST's edit_imgt_file.pl script, which truncates IMGT headers to keep only the allele designation.

Output files follow the naming convention used by IgBLAST:

<organism>_<receptor_type>_v.fasta
<organism>_<receptor_type>_d.fasta
<organism>_<receptor_type>_j.fasta

After exporting, use makeblastdb with the -parse_seqids flag to create the BLAST database:

makeblastdb -parse_seqids -dbtype nucl -in <fasta_file> -out <db_name>

This function works with sequences from both IMGT (via getIMGT) and OGRDB (via getOGRDB).

Value

A named list containing the paths to the created files, returned invisibly. The list may contain elements v_genes, d_genes, and j_genes depending on which segment types were found in the input sequences.

Examples

# Create a small example DNAStringSet
seqs <- Biostrings::DNAStringSet(c(
  "ATGCGATCGATCGATCG",
  "ATGCGATCGATCG",
  "ATGCGATC"
))
names(seqs) <- c("IGHV1-2*01", "IGHD1-1*01", "IGHJ1*01")

# Export to temporary directory
output_dir <- tempdir()
files <- exportIgBLAST(seqs, output_dir, organism = "human", receptor_type = "ig")
print(files)

# Clean up
unlink(unlist(files))
# Create a small example DNAStringSet
seqs <- Biostrings::DNAStringSet(c(
  "ATGCGATCGATCGATCG",
  "ATGCGATCGATCG",
  "ATGCGATC"
))
names(seqs) <- c("IGHV1-2*01", "IGHD1-1*01", "IGHJ1*01")

# Export to temporary directory
output_dir <- tempdir()
files <- exportIgBLAST(seqs, output_dir, organism = "human", receptor_type = "ig")
print(files)

# Clean up
unlink(unlist(files))

Export Reference Sequences to MiXCR Format

Description

Exports a DNAStringSet or AAStringSet to FASTA files formatted for use with MiXCR's buildLibrary command. The function creates separate FASTA files for V, D, J, and C gene segments.

Usage

exportMiXCR(
  sequences,
  output_dir,
  chain = c("IGH", "IGK", "IGL", "TRA", "TRB", "TRD", "TRG")
)
exportMiXCR(
  sequences,
  output_dir,
  chain = c("IGH", "IGK", "IGL", "TRA", "TRB", "TRD", "TRG")
)

Arguments

sequences

A DNAStringSet or AAStringSet object containing immune receptor sequences. Sequence names must follow standard IG/TR gene nomenclature (e.g., "IGHV1-2*01", "TRBJ2-1*01"). Can be obtained from getIMGT or getOGRDB.

output_dir

Character string specifying the directory where output files will be written. The directory will be created if it does not exist.

chain

Character string specifying the chain type for the output files. Must be one of "IGH", "IGK", "IGL", "TRA", "TRB", "TRD", or "TRG".

Details

MiXCR expects FASTA files with simple headers containing only the gene name. The function filters sequences by gene type (V, D, J, C) based on the gene name pattern and writes separate files for each segment type.

Output files follow the naming convention:

v-genes.<chain>.fasta
d-genes.<chain>.fasta
j-genes.<chain>.fasta
c-genes.<chain>.fasta

This function works with sequences from both IMGT (via getIMGT) and OGRDB (via getOGRDB).

Value

A named list containing the paths to the created files, returned invisibly. The list may contain elements v_genes, d_genes, j_genes, and c_genes depending on which segment types were found in the input sequences.

Examples

# Create a small example DNAStringSet
seqs <- Biostrings::DNAStringSet(c(
  "ATGCGATCGATCGATCG",
  "ATGCGATCGATCG",
  "ATGCGATC",
  "ATGCGATCGATCGATCGATCG"
))
names(seqs) <- c("IGHV1-2*01", "IGHD1-1*01", "IGHJ1*01", "IGHC*01")

# Export to temporary directory
output_dir <- tempdir()
files <- exportMiXCR(seqs, output_dir, chain = "IGH")
print(files)

# Clean up
unlink(unlist(files))
# Create a small example DNAStringSet
seqs <- Biostrings::DNAStringSet(c(
  "ATGCGATCGATCGATCG",
  "ATGCGATCGATCG",
  "ATGCGATC",
  "ATGCGATCGATCGATCGATCG"
))
names(seqs) <- c("IGHV1-2*01", "IGHD1-1*01", "IGHJ1*01", "IGHC*01")

# Export to temporary directory
output_dir <- tempdir()
files <- exportMiXCR(seqs, output_dir, chain = "IGH")
print(files)

# Clean up
unlink(unlist(files))

Export Reference Sequences to TRUST4 Format

Description

Exports a DNAStringSet to a FASTA file formatted for use with TRUST4. The output follows the format produced by TRUST4's BuildImgtAnnot.pl script.

Usage

exportTRUST4(sequences, output_file, include_constant = TRUE)
exportTRUST4(sequences, output_file, include_constant = TRUE)

Arguments

sequences

A DNAStringSet object containing immune receptor sequences. Sequence names must follow standard IG/TR gene nomenclature (e.g., "IGHV1-2*01"). Can be obtained from getIMGT or getOGRDB.

output_file

Character string specifying the path to the output FASTA file. The parent directory will be created if it does not exist.

include_constant

Logical. If TRUE (default), include constant region sequences. TRUST4's IMGT+C.fa file includes constant regions.

Details

TRUST4 expects FASTA files with headers containing only the allele name (e.g., >IGHV1-2*01). The function reformats sequence headers to match the output of TRUST4's BuildImgtAnnot.pl script.

TRUST4 uses this reference for the --ref parameter in its analysis pipeline.

This function works with sequences from both IMGT (via getIMGT) and OGRDB (via getOGRDB).

Value

Character string with the path to the created file, returned invisibly.

Examples

# Create a small example DNAStringSet
seqs <- Biostrings::DNAStringSet(c(
  "ATGCGATCGATCGATCG",
  "ATGCGATCGATCG",
  "ATGCGATC"
))
names(seqs) <- c("IGHV1-2*01", "IGHJ1*01", "IGHC*01")

# Export to temporary file
output_file <- tempfile(fileext = ".fa")
exportTRUST4(seqs, output_file)

# View the result
cat(readLines(output_file), sep = "\n")

# Clean up
unlink(output_file)
# Create a small example DNAStringSet
seqs <- Biostrings::DNAStringSet(c(
  "ATGCGATCGATCGATCG",
  "ATGCGATCGATCG",
  "ATGCGATC"
))
names(seqs) <- c("IGHV1-2*01", "IGHJ1*01", "IGHC*01")

# Export to temporary file
output_file <- tempfile(fileext = ".fa")
exportTRUST4(seqs, output_file)

# View the result
cat(readLines(output_file), sep = "\n")

# Clean up
unlink(output_file)

Download and Load Immune Receptor and HLA Sequences from IMGT

Description

This is the main function to download and load reference sequences from IMGT and the IPD-IMGT/HLA database. It handles caching of downloaded files.

Usage

getIMGT(
  species = "human",
  gene,
  type = c("NUC", "PROT"),
  refresh = FALSE,
  suppressMessages = FALSE
)
getIMGT(
  species = "human",
  gene,
  type = c("NUC", "PROT"),
  refresh = FALSE,
  suppressMessages = FALSE
)

Arguments

species

Character string specifying the species for which to download data. Required for TCR/BCR queries. Currently supported species: "human", "mouse", "rat", "rabbit", "pig", "dog", "rhesus_monkey", "cyno_monkey". Defaults to "human" for HLA queries.

gene

Character string specifying the gene or locus to download. For TCR/BCR, this can be a specific chain (e.g., "IGHV", "TRBJ") or a group (e.g., "IGH", "TCR"). For HLA, use "HLA".

type

Character string specifying the type of sequence to retrieve. Either "NUC" for nucleotide or "PROT" for protein sequences. This primarily distinguishes between VDJ nucleotide and V-region amino acid sequences for TCR/BCR genes.

refresh

Logical. If TRUE, forces a re-download of the data even if it exists in the cache. Default is FALSE.

suppressMessages

Logical. If TRUE, suppresses the license and other informational messages. Default is FALSE.

Value

A DNAStringSet object (when type = "NUC") or AAStringSet object (when type = "PROT") containing the requested sequences.

Examples

if(is_imgt_available()) {
  # Download human IGHV nucleotide sequences
  ighv_nuc <- getIMGT(species = "human",
                      gene = "IGHV",
                      type = "NUC")

  # Download all HLA protein sequences
  hla_prot <- getIMGT(gene = "HLA",
                      type = "PROT")

  # Download all mouse TRB genes
  trb_mouse <- getIMGT(species = "mouse",
                      gene = "TRB",
                      type = "NUC")
}

if(is_imgt_available()) {
  # Download human IGHV nucleotide sequences
  ighv_nuc <- getIMGT(species = "human",
                      gene = "IGHV",
                      type = "NUC")

  # Download all HLA protein sequences
  hla_prot <- getIMGT(gene = "HLA",
                      type = "PROT")

  # Download all mouse TRB genes
  trb_mouse <- getIMGT(species = "mouse",
                      gene = "TRB",
                      type = "NUC")
}

Download and Load Immune Receptor Germline Sequences from OGRDB

Description

Downloads AIRR-compliant germline sets (or FASTA) from OGRDB (Open Germline Receptor Database) and returns sequences as a DNAStringSet or AAStringSet.

Usage

getOGRDB(
  species = "human",
  locus = c("IGH", "IGK", "IGL"),
  set_name = NULL,
  type = c("NUC", "PROT"),
  format = c("FASTA_GAPPED", "FASTA_UNGAPPED", "AIRR"),
  version = c("published", "latest"),
  species_subgroup = NULL,
  refresh = FALSE,
  suppressMessages = FALSE
)
getOGRDB(
  species = "human",
  locus = c("IGH", "IGK", "IGL"),
  set_name = NULL,
  type = c("NUC", "PROT"),
  format = c("FASTA_GAPPED", "FASTA_UNGAPPED", "AIRR"),
  version = c("published", "latest"),
  species_subgroup = NULL,
  refresh = FALSE,
  suppressMessages = FALSE
)

Arguments

species

Character string specifying the species. Accepts "human", "Homo sapiens", "mouse", or "Mus musculus". Default is "human".

locus

Character string specifying the locus short code. One of "IGH", "IGK", or "IGL". Can be NULL if you pass a set_name explicitly.

set_name

Optional character string specifying an explicit OGRDB set name (e.g., "IGH_VDJ"). If provided, overrides locus.

type

Character string specifying the sequence type. Either "NUC" (default) for nucleotide or "PROT" for protein. "PROT" will translate V-gene CDS; only supported for FASTA or AIRR records that include a valid CDS.

format

Character string specifying the download format. One of "FASTA_GAPPED" (default), "FASTA_UNGAPPED", or "AIRR".

version

Character string specifying the version. Either "published" (default) or "latest".

species_subgroup

Optional character string specifying a subgroup (e.g., a mouse strain like "C57BL/6"). If it contains /, OGRDB requires it encoded as %252f.

refresh

Logical. If TRUE, forces re-download even if cached. Default is FALSE.

suppressMessages

Logical. If TRUE, suppresses informational messages. Default is FALSE.

Details

OGRDB (Open Germline Receptor Database) is the AIRR Community's curated repository of germline receptor sequences. It complements IMGT with additional species support and standardized AIRR JSON format.

The function supports multiple download formats:

FASTA_GAPPED: FASTA with IMGT gaps preserved
FASTA_UNGAPPED: FASTA without gaps
AIRR: AIRR-C compliant JSON format

Value

A DNAStringSet object (when type = "NUC") or AAStringSet object (when type = "PROT") containing the requested sequences.

Examples

if (is_ogrdb_available()) {
  # Download human IGH nucleotide sequences (gapped FASTA)
  igh_nuc <- getOGRDB(species = "human",
                      locus   = "IGH",
                      type    = "NUC",
                      format  = "FASTA_GAPPED")

  # Download human IGK sequences in AIRR JSON format
  igk_airr <- getOGRDB(species = "human",
                       locus   = "IGK",
                       type    = "NUC",
                       format  = "AIRR")

  # Download human IGL sequences and translate to AA
  igl_prot <- getOGRDB(species = "human",
                       locus   = "IGL",
                       type    = "PROT",
                       format  = "FASTA_UNGAPPED")

  # Example using an explicit set name (instead of locus)
  igh_explicit <- getOGRDB(species  = "human",
                           set_name = "IGH_VDJ",
                           type     = "NUC",
                           format   = "FASTA_GAPPED")
}
if (is_ogrdb_available()) {
  # Download human IGH nucleotide sequences (gapped FASTA)
  igh_nuc <- getOGRDB(species = "human",
                      locus   = "IGH",
                      type    = "NUC",
                      format  = "FASTA_GAPPED")

  # Download human IGK sequences in AIRR JSON format
  igk_airr <- getOGRDB(species = "human",
                       locus   = "IGK",
                       type    = "NUC",
                       format  = "AIRR")

  # Download human IGL sequences and translate to AA
  igl_prot <- getOGRDB(species = "human",
                       locus   = "IGL",
                       type    = "PROT",
                       format  = "FASTA_UNGAPPED")

  # Example using an explicit set name (instead of locus)
  igh_explicit <- getOGRDB(species  = "human",
                           set_name = "IGH_VDJ",
                           type     = "NUC",
                           format   = "FASTA_GAPPED")
}

Check if IMGT Website is Available

Description

Sends a lightweight HEAD request to the main IMGT page to check if the service is online and accessible. This function is used to conditionally run examples and tests that require an internet connection.

Usage

is_imgt_available()
is_imgt_available()

Value

A logical value: TRUE if the IMGT website is accessible, FALSE otherwise.

Examples

is_imgt_available()
is_imgt_available()

Check if OGRDB Website is Available

Description

Sends a lightweight HEAD request to the OGRDB API to check if the service is online and accessible. This function is used to conditionally run examples and tests that require an internet connection.

Usage

is_ogrdb_available()
is_ogrdb_available()

Value

A logical value: TRUE if the OGRDB website is accessible, FALSE otherwise.

Examples

is_ogrdb_available()
is_ogrdb_available()

List Datasets in the Local Cache

Description

Scans the cache directory and returns a list of available datasets that have been downloaded.

Usage

listIMGT()
listIMGT()

Value

A character vector of absolute file paths for the cached datasets. Returns an empty character vector if the cache directory does not exist or contains no files.

Examples

# List all files in the cache
cached_files <- listIMGT()

# To see the structure, you can print the first few
head(cached_files)
# List all files in the cache
cached_files <- listIMGT()

# To see the structure, you can print the first few
head(cached_files)

List OGRDB Datasets in Local Cache

Description

Scans the cache directory and returns a list of available OGRDB datasets that have been downloaded.

Usage

listOGRDB()
listOGRDB()

Value

A character vector of absolute file paths to cached OGRDB files. Returns an empty character vector if no OGRDB files have been cached. Paths are typically under the package cache directory (e.g., ~/.immReferent/<Species>/ogrdb/).

Examples

# List cached OGRDB files
cached_files <- listOGRDB()
head(cached_files)
# List cached OGRDB files
cached_files <- listOGRDB()
head(cached_files)

Load Cached IMGT/HLA Sequences

Description

Loads sequences from the local cache without attempting to download. This function is a convenience wrapper for getIMGT(refresh = FALSE). If the data is not found in the cache, it will be downloaded unless an internet connection is unavailable.

Usage

loadIMGT(
  species = "human",
  gene,
  type = c("NUC", "PROT"),
  suppressMessages = FALSE
)
loadIMGT(
  species = "human",
  gene,
  type = c("NUC", "PROT"),
  suppressMessages = FALSE
)

Arguments

species

gene

Character string specifying the gene or locus to download. For TCR/BCR, this can be a specific chain (e.g., "IGHV", "TRBJ") or a group (e.g., "IGH", "TCR"). For HLA, use "HLA".

type

suppressMessages

Logical. If TRUE, suppresses the license and other informational messages. Default is FALSE.

Value

A DNAStringSet object (when type = "NUC") or AAStringSet object (when type = "PROT") containing the requested sequences.

Examples

if(is_imgt_available()) {
  # First, download a file to ensure it's in the cache
  getIMGT(species = "human", gene = "IGHV", type = "NUC", suppressMessages = TRUE)
  # Now, load it from the cache
  ighv_cached <- loadIMGT(species = "human", gene = "IGHV", type = "NUC")
}
if(is_imgt_available()) {
  # First, download a file to ensure it's in the cache
  getIMGT(species = "human", gene = "IGHV", type = "NUC", suppressMessages = TRUE)
  # Now, load it from the cache
  ighv_cached <- loadIMGT(species = "human", gene = "IGHV", type = "NUC")
}

Load Cached OGRDB Sequences

Description

Loads sequences from the local cache without attempting to download. This function is a convenience wrapper for getOGRDB(refresh = FALSE). If the data is not found in the cache, it will be downloaded unless an internet connection is unavailable.

Usage

loadOGRDB(
  species = "human",
  locus = c("IGH", "IGK", "IGL"),
  set_name = NULL,
  type = c("NUC", "PROT"),
  format = c("FASTA_GAPPED", "FASTA_UNGAPPED", "AIRR"),
  version = c("published", "latest"),
  species_subgroup = NULL,
  suppressMessages = FALSE
)
loadOGRDB(
  species = "human",
  locus = c("IGH", "IGK", "IGL"),
  set_name = NULL,
  type = c("NUC", "PROT"),
  format = c("FASTA_GAPPED", "FASTA_UNGAPPED", "AIRR"),
  version = c("published", "latest"),
  species_subgroup = NULL,
  suppressMessages = FALSE
)

Arguments

species

Character string specifying the species. Accepts "human", "Homo sapiens", "mouse", or "Mus musculus". Default is "human".

locus

Character string specifying the locus short code. One of "IGH", "IGK", or "IGL". Can be NULL if you pass a set_name explicitly.

set_name

Optional character string specifying an explicit OGRDB set name (e.g., "IGH_VDJ"). If provided, overrides locus.

type

format

Character string specifying the download format. One of "FASTA_GAPPED" (default), "FASTA_UNGAPPED", or "AIRR".

version

Character string specifying the version. Either "published" (default) or "latest".

species_subgroup

Optional character string specifying a subgroup (e.g., a mouse strain like "C57BL/6"). If it contains /, OGRDB requires it encoded as %252f.

suppressMessages

Logical. If TRUE, suppresses informational messages. Default is FALSE.

Value

A DNAStringSet object (when type = "NUC") or AAStringSet object (when type = "PROT") containing the requested sequences.

Examples

if (is_ogrdb_available()) {
  # First, ensure the file is cached
  getOGRDB(species = "human", locus = "IGH",
           type = "NUC", format = "FASTA_GAPPED",
           suppressMessages = TRUE)

  # Now load from cache only
  igh_cached <- loadOGRDB(species = "human",
                          locus   = "IGH",
                          type    = "NUC",
                          format  = "FASTA_GAPPED")
}
if (is_ogrdb_available()) {
  # First, ensure the file is cached
  getOGRDB(species = "human", locus = "IGH",
           type = "NUC", format = "FASTA_GAPPED",
           suppressMessages = TRUE)

  # Now load from cache only
  igh_cached <- loadOGRDB(species = "human",
                          locus   = "IGH",
                          type    = "NUC",
                          format  = "FASTA_GAPPED")
}

Force Re-download of IMGT/HLA Sequences

Description

A convenience wrapper for getIMGT(..., refresh = TRUE) to ensure that the local cache is updated with the latest versions of the requested sequences.

Usage

refreshIMGT(
  species = "human",
  gene,
  type = c("NUC", "PROT"),
  suppressMessages = FALSE
)
refreshIMGT(
  species = "human",
  gene,
  type = c("NUC", "PROT"),
  suppressMessages = FALSE
)

Arguments

species

gene

Character string specifying the gene or locus to download. For TCR/BCR, this can be a specific chain (e.g., "IGHV", "TRBJ") or a group (e.g., "IGH", "TCR"). For HLA, use "HLA".

type

suppressMessages

Logical. If TRUE, suppresses the license and other informational messages. Default is FALSE.

Value

A DNAStringSet object (when type = "NUC") or AAStringSet object (when type = "PROT") containing the requested sequences.

Examples

if(is_imgt_available()) {
  # Force a re-download of human IGHV protein sequences
  ighv_prot_fresh <- refreshIMGT(species = "human", gene = "IGHV", type = "PROT")
}
if(is_imgt_available()) {
  # Force a re-download of human IGHV protein sequences
  ighv_prot_fresh <- refreshIMGT(species = "human", gene = "IGHV", type = "PROT")
}

Force Re-download of OGRDB Sequences

Description

A convenience wrapper for getOGRDB(..., refresh = TRUE) to ensure that the local cache is updated with the latest versions of the requested sequences.

Usage

refreshOGRDB(
  species = "human",
  locus = c("IGH", "IGK", "IGL"),
  set_name = NULL,
  type = c("NUC", "PROT"),
  format = c("FASTA_GAPPED", "FASTA_UNGAPPED", "AIRR"),
  version = c("published", "latest"),
  species_subgroup = NULL,
  suppressMessages = FALSE
)
refreshOGRDB(
  species = "human",
  locus = c("IGH", "IGK", "IGL"),
  set_name = NULL,
  type = c("NUC", "PROT"),
  format = c("FASTA_GAPPED", "FASTA_UNGAPPED", "AIRR"),
  version = c("published", "latest"),
  species_subgroup = NULL,
  suppressMessages = FALSE
)

Arguments

species

Character string specifying the species. Accepts "human", "Homo sapiens", "mouse", or "Mus musculus". Default is "human".

locus

Character string specifying the locus short code. One of "IGH", "IGK", or "IGL". Can be NULL if you pass a set_name explicitly.

set_name

Optional character string specifying an explicit OGRDB set name (e.g., "IGH_VDJ"). If provided, overrides locus.

type

format

Character string specifying the download format. One of "FASTA_GAPPED" (default), "FASTA_UNGAPPED", or "AIRR".

version

Character string specifying the version. Either "published" (default) or "latest".

species_subgroup

Optional character string specifying a subgroup (e.g., a mouse strain like "C57BL/6"). If it contains /, OGRDB requires it encoded as %252f.

suppressMessages

Logical. If TRUE, suppresses informational messages. Default is FALSE.

Value

A DNAStringSet object (when type = "NUC") or AAStringSet object (when type = "PROT") containing the requested sequences.

Examples

if (is_ogrdb_available()) {
  # Force a re-download of the human IGK sequences
  igk_fresh <- refreshOGRDB(species = "human",
                            locus   = "IGK",
                            type    = "NUC",
                            format  = "FASTA_GAPPED")
}
if (is_ogrdb_available()) {
  # Force a re-download of the human IGK sequences
  igk_fresh <- refreshOGRDB(species = "human",
                            locus   = "IGK",
                            type    = "NUC",
                            format  = "FASTA_GAPPED")
}

Package 'immReferent'

Help Index

immReferent: An Interface for Immune Receptor and HLA Gene Reference Data

Description

Details

Attribution and Licensing

Author(s)

See Also

Export Reference Sequences to Cell Ranger VDJ Format

Description

Usage

Arguments

Details

Value

See Also

Examples

Export Reference Sequences to IgBLAST Format

Description

Usage

Arguments

Details

Value

See Also

Examples

Export Reference Sequences to MiXCR Format

Description

Usage

Arguments

Details

Value

See Also

Examples

Export Reference Sequences to TRUST4 Format

Description

Usage

Arguments

Details

Value

See Also

Examples

Download and Load Immune Receptor and HLA Sequences from IMGT

Description

Usage

Arguments

Value

See Also

Examples

Download and Load Immune Receptor Germline Sequences from OGRDB

Description

Usage

Arguments

Details

Value

See Also

Examples

Check if IMGT Website is Available

Description

Usage

Value

See Also

Examples

Check if OGRDB Website is Available

Description

Usage

Value

See Also

Examples

List Datasets in the Local Cache

Description

Usage

Value

See Also

Examples

List OGRDB Datasets in Local Cache

Description

Usage

Value

See Also

Examples

Load Cached IMGT/HLA Sequences