BiocRefgetStore Reference

Complete reference for every exported function, method, and class in BiocRefgetStore.

Constructors

RefgetGenome.from_fasta

RefgetGenome.from_fasta(fasta_path)

Create a RefgetGenome from a FASTA file. Builds an in-memory refget store, computes digests, and indexes all sequences.

• fasta_path — Path to a FASTA file (.fa, .fasta, .fa.gz).
• Returns — A RefgetGenome object.

genome <- RefgetGenome.from_fasta("hg38.fa")

RefgetGenome.from_directory

RefgetGenome.from_directory(path, digest = NULL, namespace = NULL, alias = NULL)

Load a RefgetGenome from a persisted on-disk refget store directory.

• path — Path to a directory created by gtars::refget_store_on_disk().
• digest — Collection digest string (provide this OR namespace + alias).
• namespace — Alias namespace (e.g., "refseq").
• alias — Alias name (e.g., "GRCh38").
• Returns — A RefgetGenome object.

genome <- RefgetGenome.from_directory("~/.refget/hg38", digest = "abc123...")

RefgetGenome.from_remote

RefgetGenome.from_remote(cache_path, remote_url, digest = NULL, namespace = NULL, alias = NULL)

Create a RefgetGenome backed by a remote refget store with local caching.

• cache_path — Local directory for caching downloaded data.
• remote_url — URL of the remote refget store.
• digest / namespace / alias — Same as RefgetGenome.from_directory.
• Returns — A RefgetGenome object.

genome <- RefgetGenome.from_remote(
  cache_path = "~/.cache/refget/pangenome",
  remote_url = "https://refgenie.s3.us-east-1.amazonaws.com/pangenome_refget_store",
  digest = "0qveCdMlbF_kYn6XWb7YBy-FtRZ6gSAL"
)

RefgetGenome (low-level)

RefgetGenome(store, digest = NULL, namespace = NULL, alias = NULL)

Construct a RefgetGenome from an existing gtars::RefgetStore object. Requires either digest or both namespace and alias.

• store — A gtars RefgetStore object.
• digest / namespace / alias — Collection identifier.
• Returns — A RefgetGenome object.

store <- gtars::refget_store_open_local("/path/to/store")
genome <- RefgetGenome(store, namespace = "refseq", alias = "GRCh38")

---

Sequence Access

getSeq

getSeq(x, names, start = NA, end = NA, strand = "+", as.character = FALSE, ...)

Extract sequences from a RefgetGenome. BSgenome-compatible interface.

• x — A RefgetGenome object.
• names — Character vector of sequence names, or a GRanges object.
• start — Integer start position(s), 1-based inclusive. NA for full sequence.
• end — Integer end position(s), 1-based inclusive. NA for full sequence.
• strand — "+" (default) or "-" for reverse complement.
• as.character — If TRUE, return character instead of DNAString/DNAStringSet.
• Returns — Single sequence: DNAString (or character). Multiple: DNAStringSet (or character vector). Named as "seqname:start-end" for regions.

getSeq(genome, "chr1")

# Region
getSeq(genome, "chr1", start = 100, end = 200)

# Reverse complement
getSeq(genome, "chr1", start = 100, end = 200, strand = "-")

# Multiple regions
getSeq(genome, c("chr1", "chr2"), c(100, 500), c(200, 600))

# From GRanges
getSeq(genome, GRanges("chr1:100-200:-"))

[[ (bracket extraction)

genome[["chr1"]]

Extract a full sequence by name. Returns a DNAString.

• i — Sequence name (character).
• Returns — DNAString or character string.
• Errors — If the sequence name is not found in the collection.

---

Metadata Accessors

seqinfo

seqinfo(x)

Returns the Seqinfo object containing sequence names and lengths.

• Returns — A GenomeInfoDb::Seqinfo object.

seqnames

seqnames(x)

Returns the sequence names.

• Returns — Character vector (via Seqinfo).

seqlengths

seqlengths(x)

Returns named integer vector of sequence lengths.

• Returns — Named integer vector.

seqlengths(genome)
#>   chr1   chr2   chr3
#> 248956 242193 198295

length

length(x)

Returns the number of sequences in the genome.

• Returns — Integer scalar.

names

names(x)

Returns the sequence names as a character vector.

• Returns — Character vector.

collection_digest

collection_digest(genome)

Returns the GA4GH seqcol digest identifying this sequence collection.

• genome — A RefgetGenome object.
• Returns — Character string.

coordinate_system

coordinate_system(genome)

Returns the sorted_name_length_pairs digest. Two genomes with the same coordinate_system() share the same coordinate system and are compatible for coordinate-based operations (e.g., lifting over annotations).

• genome — A RefgetGenome object.
• Returns — Character string.

sequence_digests

sequence_digests(genome)

Returns a named character vector of per-sequence SHA512t24u digests.

• genome — A RefgetGenome object.
• Returns — Named character vector (names are sequence names, values are digests).

sequence_digests(genome)
#>                         chr1                          chr2
#> "SQ.2648ae1bacce4ec4b6cf337..." "SQ.f932a39b4c70..."

store

store(genome)

Returns the underlying gtars::RefgetStore object. Useful for calling gtars functions directly.

• genome — A RefgetGenome object.
• Returns — A gtars RefgetStore object.

---

Bulk Extraction

extractRegions

extractRegions(genome, regions, as.character = FALSE)

Extract multiple genomic regions efficiently using BED-based extraction.

• genome — A RefgetGenome object.
• regions — A GRanges object or a data.frame with columns chrom, start, end (1-based inclusive coordinates).
• as.character — If TRUE, return character vector instead of DNAStringSet.
• Returns — DNAStringSet or named character vector. Named as "chrom:start-end".

regions <- data.frame(
  chrom = c("chr1", "chr1", "chr2"),
  start = c(100, 5000, 200),
  end   = c(199, 5099, 299)
)
seqs <- extractRegions(genome, regions)

extractToFasta

extractToFasta(genome, regions, output_path)

Write extracted regions directly to a FASTA file.

• genome — A RefgetGenome object.
• regions — A GRanges object or data.frame (same as extractRegions).
• output_path — Path for the output FASTA file.
• Returns — Invisibly returns output_path.

extractToFasta(genome, regions, "output.fa")

exportChromosomes

exportChromosomes(genome, names = NULL, output_path, line_width = 80L)

Export complete chromosomes to a FASTA file.

• genome — A RefgetGenome object.
• names — Character vector of chromosome names to export, or NULL for all.
• output_path — Path for the output FASTA file.
• line_width — Bases per line in output (default: 80).
• Returns — Invisibly returns output_path.

# Specific chromosomes
exportChromosomes(genome, c("chr1", "chr22"), "subset.fa")

# All chromosomes
exportChromosomes(genome, output_path = "full.fa")

---

Conversion Utilities

as_DNAString

as_DNAString(seq_string)

Convert a character string to a Biostrings DNAString object.

• seq_string — Character string containing a DNA sequence.
• Returns — A DNAString object.

dna <- as_DNAString("ACGTACGT")

as_DNAStringSet

as_DNAStringSet(seq_strings, names = NULL)

Convert a character vector to a Biostrings DNAStringSet object.

• seq_strings — Character vector of DNA sequences.
• names — Optional names for the sequences.
• Returns — A DNAStringSet object.

seqs <- as_DNAStringSet(c("ACGT", "GGCC"), names = c("seq1", "seq2"))

---

BSgenome Conversion

forgeBSgenome

forgeBSgenome(genome, pkg_name, organism, common_name = organism,
              circ_seqs = character(0), version = "1.0.0",
              dest = ".", replace = FALSE)

Build an installable BSgenome data package from a RefgetGenome. Requires BSgenomeForge. The collection digest is recorded as the package's genome field.

• pkg_name — BSgenome.<Abbrev>.<provider>.<build>; <Abbrev> becomes the exported object name.
• organism — Scientific name, e.g. "Homo sapiens".
• circ_seqs — Names of circular sequences such as "chrM".
• Returns — Invisibly, the path to the new package directory.

pkg <- forgeBSgenome(genome, "BSgenome.Hsapiens.refget.GRCh38",
                     organism = "Homo sapiens", circ_seqs = "chrM",
                     dest = tempdir())
install.packages(pkg, repos = NULL, type = "source")

RefgetGenome.from_bsgenome

RefgetGenome.from_bsgenome(bsgenome, names = NULL)

Load a BSgenome into a new in-memory RefgetStore. A genome forged with forgeBSgenome() and loaded back gets the same collection digest.

• bsgenome — A BSgenome object.
• names — Optional sequence names to include (NULL = all).
• Returns — A RefgetGenome.

library(BSgenome.Hsapiens.UCSC.hg38)
genome <- RefgetGenome.from_bsgenome(BSgenome.Hsapiens.UCSC.hg38)

Working with the Underlying Store

The store() accessor gives you access to the full gtars::RefgetStore API for operations not directly exposed by BiocRefgetStore.

s <- store(genome)

# List all aliases in the store
gtars::get_aliases(s)

# Compare two sequence collections
gtars::compare_seqcols(s, digest_a, digest_b)

# Get FHR (FASTA Header Record) metadata
gtars::get_fhr(s, collection_digest(genome))

# Access level 2 data (raw attribute arrays)
level2 <- gtars::get_level2(s, collection_digest(genome))
level2$names      # sequence names
level2$lengths    # sequence lengths
level2$sequences  # sequence digests

show

show(object)

Display method for RefgetGenome. Prints the number of sequences, collection digest, and first few sequence names.

genome
#> RefgetGenome with 24 sequences
#>   collection_digest: abc123...
#>   seqnames: chr1, chr2, chr3, chr4, chr5 ... (19 more)