Import MZmine feature table and metadata to create a mmo object

Reads an MZmine exported feature table (typically the full feature table) and a sample metadata table to initialize an mmo object containing:

mmo$feature_data: feature-by-sample abundance matrix (peak areas)
mmo$feature_info: feature-level annotations (e.g., mz, rt, ranges, IDs)
mmo$metadata: sample metadata with standardized sample and group columns

Sample columns in the MZmine table are matched to metadata using fuzzy string matching on area column names.

Usage

GetMZmineFeature(
  mzmine_dir,
  metadata_dir,
  group_col,
  sample_col,
  drop_missing_samples = FALSE,
  mz_col = NULL,
  rt_col = NULL,
  max_distance = 5,
  pa_threshold = 1,
  feature_info_cols = c("id", "rt", "rt_range:min", "rt_range:max", "mz", "mz_range:min",
    "mz_range:max", "feature_group", "ion_identities:iin_id",
    "ion_identities:ion_identities")
)

Arguments

mzmine_dir: Path to the MZmine feature table CSV (should include feature-level columns and per-sample area columns)
metadata_dir: Path to the metadata CSV file (must include sample_col and group_col)
group_col: Column name in metadata used for grouping samples (e.g., treatment/species)
sample_col: Column name in metadata used to identify and match samples to MZmine area columns
drop_missing_samples: Logical. If FALSE (default), error when metadata samples are missing from the MZmine table area columns. If TRUE, drop those samples from metadata (with a warning) and continue.
mz_col: Optional m/z column name in the MZmine table (defaults to "mz" or "row m/z")
rt_col: Optional RT column name in the MZmine table (defaults to "rt" or "row retention time")
max_distance: Maximum edit distance used when fuzzy-matching metadata sample names to MZmine area column names (default 5). Lower this for stricter matching.
pa_threshold: Minimum peak area threshold for a feature to be considered present in a sample.
feature_info_cols: Character vector of feature-level columns to retain in mmo$feature_info. Columns not present in the MZmine table are skipped with a warning.

Value

A mmo object