Build ratio-shift data from multi-instrument PAVE2 files — build_instrument_ratio_shift

Loads precomputed PAVE2 MSdev objects, extracts CN seed labeling ratios, and computes ratio shift relative to the 1:1:1:1 intensity assumption. Results are cached as RDS under `cache_dir` and reused when source files are unchanged.

Usage

build_instrument_ratio_shift_data(
  data_dir = "d:/data/2025.12.26.PAVE2/PAVE_With_Params/",
  pattern = "ppm10_sn10.rdata",
  exclude_instru = "Exd_480K_eDR",
  cor_cutoff = 0.75,
  instru_levels = .cor_sens_default_instru_levels(),
  use_cache = TRUE,
  cache_dir = NULL,
  cache_file = NULL
)

Arguments

data_dir: Directory containing `*_ppm10_sn10.rdata` instrument files.
pattern: Filename pattern passed to [base::dir()].
exclude_instru: Character vector of instrument name substrings to skip.
cor_cutoff: Minimum `pave_cor` for CN seeds.
instru_levels: Factor levels for `instru.name`.
use_cache: If `TRUE`, read or write an RDS cache in `cache_dir`.
cache_dir: Directory for cached RDS files. Defaults to `file.path(TRACE_PKG_ROOT or getwd(), "cache")`.
cache_file: Optional explicit RDS path (overrides the default name).

Value

A data frame with columns `instru.name`, `polarity`, `TRACE_seed`, `TRACE_formula`, `TRACE_cor`, `seed_intensity`, `label_group`, `feature_id`, `adduct_form`, `group_ratio`, `ratio_shift`, `log10_intensity`, and `intensity_bin`.