Frozen Reference Datasets

isoformic ships evidence tables derived from public resources, frozen at a given version so that results are reproducible:

• appris: APPRIS principal/alternative isoform labels and method scores (functional residues, structure, conservation, domains) per transcript, from the APPRIS release files.

• appris_domains: Pfam domain genomic coordinates per transcript (APPRIS SPADE).

• riboseq_orfs: GENCODE Ribo-seq ORF catalog, phase 1 and phase 2, with exon blocks and compatible transcripts.

• nmd_exons: NMD-inducing cassette exons validated by NMD inhibition and nanopore sequencing (Karousis et al. 2021, Genome Biology, Supplementary Table 1).

• polyasite: PolyASite 2.0 poly(A) site atlas (GRCh38) with site class and poly(A) signals.

• gtex_transcript_tpm: GTEx v8 median transcript TPM per tissue (RSEM).

frozen_datasets() lists them with version, source URLs and the MD5 of the frozen file. fetch_frozen_data() returns the local path of a dataset, downloading the frozen file from the first mirror that has it (frozen_mirrors(): any URL in options(isoformic.frozen_mirrors = ), the package's GitHub release, then the Zenodo snapshot of the processed files) or, when that is not possible (build = "auto") or asked for (build = "always"), rebuilding it from the source files with the matching build_frozen_*() function. read_frozen_data() fetches and reads it. bundle_frozen_data() assembles the snapshot that is deposited on Zenodo: every frozen file, the coding potential model, an MD5SUMS file and a README stating versions and sources.

Usage

frozen_datasets()

frozen_mirrors(
  release_tag = "frozen-data",
  zenodo_record = frozen_zenodo_record()
)

fetch_frozen_data(
  name,
  output_path = ":cache:",
  build = c("auto", "never", "always"),
  verify = TRUE,
  release_tag = "frozen-data",
  mirrors = frozen_mirrors(release_tag),
  ...
)

read_frozen_data(
  name,
  output_path = ":cache:",
  build = c("auto", "never", "always"),
  ...
)

bundle_frozen_data(
  output_dir,
  output_path = ":cache:",
  build = c("auto", "never", "always"),
  include_coding_model = TRUE,
  verify = TRUE
)

Arguments

release_tag

Tag of the GitHub release hosting the frozen files.

zenodo_record

Zenodo record id (or https://zenodo.org/records/<id> URL) of a deposit holding the frozen files; defaults to the record published with the package, NA when there is none.

name

Dataset name, one of names(frozen_datasets()).

output_path

Directory holding the frozen files; ":cache:" (default) uses get_isoformic_cache("frozen").

build

"auto" (download, else build from sources), "never" or "always".

verify

Logical, check the MD5 of the file against the registry (default TRUE; a mismatch is a warning, since a rebuilt file from a newer source is still usable).

mirrors

Character vector of base URLs tried in order for the frozen file; default frozen_mirrors().

...

Reserved for future use; must be empty.

output_dir

Directory receiving the bundle (created if needed).

include_coding_model

Logical, also copy the coding potential model files (default TRUE).

Value

frozen_datasets() returns a tibble; fetch_frozen_data() the file path, invisibly; read_frozen_data() a tibble; frozen_mirrors() a character vector; bundle_frozen_data() the bundle directory, invisibly.

Examples

frozen_datasets()[, c("name", "version", "file")]
#> # A tibble: 6 × 3
#>   name                version       file                                        
#>   <chr>               <chr>         <chr>                                       
#> 1 appris              e113v49       appris_e113v49.parquet                      
#> 2 appris_domains      e113v49       appris_domains_e113v49.parquet              
#> 3 riboseq_orfs        phase1_phase2 gencode_riboseq_orfs_phase1_phase2.parquet  
#> 4 nmd_exons           karousis2021  nmd_exons_karousis2021.parquet              
#> 5 polyasite           2.0_GRCh38.96 polyasite_2.0_GRCh38.96.parquet             
#> 6 gtex_transcript_tpm v8            gtex_v8_transcript_tpm_median_by_tissue.par…
if (FALSE) { # \dontrun{
appris <- read_frozen_data("appris")
head(appris)
} # }