SpectraToQueries

SpectraToQueries 0.0.9002

Data & Documentation

• Added clean data/ objects for standard spectra:
  • spectra_grouped (352KB): Example dataset, 321 grouped Spectra from MIADB, 53 unique skeletons
  • spectra (354KB): Ungrouped variant for comparison
  • Both fully documented with @format, @source, and usage examples
  • Load via data(spectra_grouped) or data(spectra) instead of readRDS() + system.file()
• spectra_to_queries() API improvements:
  • spectra = NULL now loads spectra_grouped automatically (cleaner default)
  • spectra = "grouped" alias for explicit grouped-data loading
  • Accepts file paths and Spectra objects as before
  • Updated roxygen with concrete usage examples
• Cleaned R/data.R:
  • Removed all inst/extdata/ system paths from examples
  • Added concrete example showing data(spectra_grouped) usage
  • Marked examples as \dontrun to avoid long test times in check

Dependencies

• Removed unnecessary fastmatch and stringi dependencies by switching those fixed-string and set-membership operations to base R.
• tidytable remains for grouping/summarization in fix_binned_mzs.R.
• Removed direct BiocParallel, data.table, progress, purrr, and tibble dependency (tidytable already in imports)

SpectraToQueries 0.0.9001

• Updated minimal R version to 4.4.0 (and related Bioconductor dependencies)

SpectraToQueries 0.0.9000

• Initial version.