CN bundle max errors for manual library-assignment types — compare_pave_lib_assignment_error

Reads a curated assignment table (e.g. compare_pave_assigment.xlsx) and joins each feature's CN-bundle max m/z error (ppm) and RT error (s) from object@advancedAna$TRACE_temp.

Usage

compare_pave_lib_assignment_error_data(
  assignment,
  object,
  i.pol = 0,
  mz_error = c("max", "mean"),
  types = NULL,
  scatter_groups = NULL
)

Arguments

assignment: Path to assignment xlsx or data frame with feature_id and type.
object: MSdev object with TRACE CNfinder results.
i.pol: Polarity index. `0` for negative and `1` for positive.
mz_error: Use `"max"` or `"mean"` across CN-bundle edges.
types: Character vector of type labels to compare. Used when scatter_groups is NULL.
scatter_groups: Optional character vector of scatter colour groups (overlap, wrong in PAVE, wrong in TRACE, filter out to noise). Requires a reason column in assignment.

Value

Data frame with feature_id, type, cn_bundle_mz_ppm, cn_bundle_rt_diff, and optionally reason / scatter_group.