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)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 Path to raw features file (CSV/TSV). |
output
|
character Path where prepared features should be saved. |
candidates
|
integer Number of top-intensity samples to retain per feature (default: from params; recommended ≤5 to balance data size and coverage). |
name_adduct
|
character Name of the adduct column in input. |
name_features
|
character Name of the feature ID column in input. |
name_rt
|
character Name of the retention time column in input. |
name_mz
|
character Name of the m/z column in input. |
Value
character(1) Path to the prepared feature table (invisibly).
See Also
Other preparation: prepare_annotations_gnps(), prepare_annotations_mzmine(), prepare_annotations_sirius(), prepare_annotations_spectra(), prepare_features_components(), prepare_features_edges(), prepare_libraries_rt(), prepare_libraries_sop_bigg(), prepare_libraries_sop_closed(), prepare_libraries_sop_ecmdb(), prepare_libraries_sop_hmdb(), prepare_libraries_sop_lotus(), prepare_libraries_sop_merged(), prepare_libraries_spectra(), prepare_params(), prepare_taxa()