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Per-feature library mismatch diagnosis (PAVE-only and TRACE-only)

Source: R/compare.pave.R
compare_pave_lib_miss_detail.Rd

Joins post-hoc chem_lib hits with TRACE pipeline status (CN dynamic filter, seed network, global assignment), metabolite/adduct role (M/A), and cpdb candidate counts at feature and seed m/z.

Usage

compare_pave_lib_miss_detail(
  pave.trace.merged.lib,
  object,
  pave.trace.merged = NULL,
  i.pol = 0,
  cpdb_path,
  rt.tol = 60,
  types = c("Metabolite", "Adduct"),
  ppm = 10
)

Arguments

pave.trace.merged.lib

Output of [.compare_pave_lib_merge()].

object

MSdev object after `TRACE_workflow()` / annotate.

pave.trace.merged

Optional PAVE/TRACE feature merge from section 2.1.

i.pol

Polarity index (`0` = negative).

cpdb_path

Path to TRACE compound database xlsx used for annotation.

rt.tol

RT tolerance in seconds (must match library merge).

types

Feature types to include (default metabolite and adduct).

ppm

m/z tolerance for adduct seed and cpdb matching.

Value

A list with `detail` (one row per mismatch feature), `summary` (counts by `summary_reason`), `pave_miss`, and `trace_miss`.