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Build the Frozen Datasets from Their Sources

Source: R/frozen-data.R
build_frozen_data.Rd

Each function downloads the source files of one frozen dataset (see frozen_datasets()) into the sources cache, converts them to the Parquet table used by the package and returns the file path. They are what fetch_frozen_data() runs when a frozen file cannot be downloaded, and what data-raw/build_frozen_data.R runs to publish a new version. The resulting tables:

  • build_frozen_appris(): one row per transcript with appris_annotation (PRINCIPAL:1 to ALTERNATIVE:2, MINOR), appris_score, the method scores (firestar_residues, matador_structure, corsair_conservation, spade_domain_score, thump_tm_helices, crash_signal, trifid_score), protein_length, ccds_id and mane label.

  • build_frozen_appris_domains(): one row per Pfam domain per transcript with its genomic span (seqid, start_pos, end_pos, strand), pfam_acc, pfam_name, evalue, pep_start, pep_end.

  • build_frozen_riboseq_orfs(): one row per Ribo-seq ORF with phase, genomic span, block_starts/block_ends (1-based, ;-separated), orf_type, gene_id, gene_name, transcript_ids (compatible transcripts, phase 1 only), replicated and studies.

  • build_frozen_nmd_exons(): one row per validated NMD-inducing exon with seqid, start_pos, end_pos, strand, the flanking exons, nmd_transcript_ids, non_nmd_transcript_ids, gene_id, gene_name. Reading the supplementary spreadsheet needs the readxl package.

  • build_frozen_polyasite(): one row per poly(A) site cluster with seqid, start_pos, end_pos, cleavage_pos, strand, tpm, frac_samples, n_protocols, site_class (TE terminal exon, EX exon, IN intron, DS downstream, AE/AI/AU antisense, IG intergenic) and signals.

  • build_frozen_gtex(): one row per transcript and tissue with median_tpm and n_samples (GTEx v8, RSEM transcript TPM; identifiers are GENCODE v26, stored without version).

Usage

build_frozen_appris(output_path = ":cache:", sources_dir = NULL)

build_frozen_appris_domains(output_path = ":cache:", sources_dir = NULL)

build_frozen_riboseq_orfs(output_path = ":cache:", sources_dir = NULL)

build_frozen_nmd_exons(output_path = ":cache:", sources_dir = NULL)

build_frozen_polyasite(output_path = ":cache:", sources_dir = NULL)

build_frozen_gtex(output_path = ":cache:", sources_dir = NULL)

Arguments

output_path

Directory receiving the Parquet file (default: the frozen-data cache).

sources_dir

Directory holding (or receiving) the source files; default: get_isoformic_cache("sources", <name>).

Value

The path of the written Parquet file, invisibly.

Examples

if (FALSE) { # \dontrun{
build_frozen_riboseq_orfs()
} # }