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Retrieve the peptide metadata table into DuckDB, forcing atomic types

Source: R/peptide-library.R
get_peptide_library.Rd

This function uses the phiperio logging utilities for consistent, ASCII-only progress messages and timing. Long-running steps are bracketed with .ph_with_timing(), and informational/warning/error messages are emitted via .ph_log_info(), .ph_log_ok(), .ph_warn(), and .ph_abort().

  • Downloads each requested library RDS once, sanitizes types (logical, character, numeric), and writes it into a DuckDB cache on disk.

  • Subsequent calls return a lazy tbl_dbi without loading into R memory.

Usage

get_peptide_library(library = "combined", force_refresh = FALSE)

Arguments

library

Character vector naming the libraries to retrieve: "combined" (agilent, twist and corona2 peptides), "human_proteome", and/or "icam". Several names return one table stacking those libraries.

force_refresh

Logical. If TRUE, re-downloads and rebuilds the cache.

Value

A dplyr::tbl_dbi pointing to the requested library: the peptide_meta_<name> table for a single library, or a view stacking the tables of several. The returned object carries an attribute "duckdb_con" with the open DBI connection.

Details

Caching: A persistent DuckDB database is created under the user cache directory (via tools::R_user_dir("phiperio", "cache")). You can override this location with options(phiperio.cache_dir = \"...\"). Each library is stored in its own peptide_meta_<name> table. The force_refresh argument bypasses the fast path and rebuilds the cache.

Several libraries: The libraries are stacked by column name in a view named after them (e.g. peptide_meta_combined_icam). Columns that only some libraries have are NA for the peptides of the others. Peptide IDs carry a library-specific prefix, so they do not collide.

Sanitization: Columns are stripped of attributes, list-columns are flattened, textual "NaN" and numeric NaN are coerced to NA. Binary 0/1 fields are converted to logical, "TRUE"/"FALSE" (case-insensitive) are converted to logical, and numeric-looking character columns (beyond trivial 0/1) are converted to numeric. All other atomic types are preserved.

Integrity check: If a SHA-256 checksum is provided, a warning is logged when the downloaded file’s checksum does not match the expected value.

See also

dplyr::tbl(), DBI::dbConnect(), duckdb::duckdb()

Examples

lib <- get_peptide_library()
#> [13:09:20] INFO  Retrieving peptide metadata into DuckDB cache
#>                  -> get_peptide_library(library = combined, force_refresh =
#>                     FALSE)
#> duckdb keeps downloaded extensions and secrets in a temporary directory:
#> ℹ /tmp/Rtmpx3O1yL/duckdb
#> This is removed when the R session ends.
#> • Extensions are re-downloaded each session.
#> • Secrets are lost.
#> ℹ Run duckdb(shared_home = TRUE) (or create ~/.duckdb) to keep them (suitable for most users).
#> ℹ Run duckdb(shared_home = FALSE) to accept the temporary directory (and silence this message).
#> ℹ See ?duckdb_storage for details and alternatives.
#> [13:09:20] INFO  Opened DuckDB connection
#>                    - cache dir:
#>                      /home/runner/.cache/R/phiperio/peptide_meta/phip_cache.duckdb
#>                    - tables: peptide_meta_combined
#> [13:09:20] OK    Using cached peptide_meta_combined (fast path)
#> [13:09:20] OK    Retrieving peptide metadata into DuckDB cache - done
#>                  -> elapsed: 0.024s