Run the refactored TRACE workflow
Usage
TRACE_workflow(
object,
rt.tol = 10,
ppm = 5,
cpdb = "d:/data/2025.12.26.PAVE2/trace.cp.db.xlsx",
eval_top = 0.2,
ratio.plot = FALSE,
ratio.reconstruct = TRUE,
dyn_rt_filter = TRUE,
pave_like = TRUE,
rt_tol_lib = 60
)Arguments
- object
MSdev object.
- rt.tol
RT tolerance in seconds.
- ppm
m/z tolerance in ppm.
- cpdb
Path to compound table xlsx used for candidate assignment.
- eval_top
Proportion in `(0, 1]` passed to `TRACE_CN_labelling_ratio_adjust()` for top-`TRACE_cor` ratio evaluation.
- ratio.plot
Logical. If `TRUE`, draw the CN labelling-ratio plot in `TRACE_CN_labelling_ratio_adjust()`.
- ratio.reconstruct
Logical. If `TRUE`, re-run `TRACE_get_CN_net()` with evaluated group ratios after CN net construction.
- dyn_rt_filter
Logical. Passed to `TRACE_dynamic_filter()`. If `FALSE`, CN seeds are not removed by the dynamic RT tolerance.
- pave_like
Logical. Passed to `TRACE_annotate()`. If `TRUE`, library assignment prefers protonated adducts, does not require MS-network adduct-edge agreement, and inherits seed-metabolite assignments for adducts.
- rt_tol_lib
RT tolerance in seconds passed to `TRACE_annotate()` for cpdb library matching.