Prepare features table

Description

Prepares LC-MS feature tables by standardizing column names, filtering to top-intensity samples per feature, and formatting for downstream analysis. Supports multiple formats (MZmine, SLAW, SIRIUS).

Usage

prepare_features_tables(
  features = get_params(step = "prepare_features_tables")\$files\$features\$raw,
  output = get_params(step = "prepare_features_tables")\$files\$features\$prepared,
  candidates = get_params(step = "prepare_features_tables")\$annotations\$canidates\$samples,
  name_adduct = get_params(step = "prepare_features_tables")\$names\$adduct,
  name_features = get_params(step = "prepare_features_tables")\$names\$features,
  name_rt = get_params(step = "prepare_features_tables")\$names\$rt\$features,
  name_mz = get_params(step = "prepare_features_tables")\$names\$precursor
)

Arguments

features	character(1) Path to raw features file (CSV/TSV).
output	character(1) Path where prepared features should be saved.
candidates	integer(1) Number of top-intensity samples to retain per feature (default: from params; recommended ≤5 to balance data size and coverage).
name_adduct	character(1) Name of the adduct column in input.
name_features	character(1) Name of the feature ID column in input.
name_rt	character(1) Name of the retention time column in input.
name_mz	character(1) Name of the m/z column in input.

Value

character(1) Path to the prepared feature table (invisibly).

Examples

library("tima")

copy_backbone()
go_to_cache()
get_file(
  url = get_default_paths()$urls$examples$features,
  export = get_params(step = "prepare_features_tables")$files$features$raw
)
prepare_features_tables()
unlink("data", recursive = TRUE)