library("tima")
copy_backbone()
go_to_cache()
prepare_annotations_gnps()
unlink("data", recursive = TRUE)Prepare annotations GNPS
Description
This function prepares GNPS spectral library matching results by standardizing column names, integrating structure metadata, and formatting for downstream TIMA annotation workflows.
Usage
prepare_annotations_gnps(
input = get_params(step =
"prepare_annotations_gnps")\$files\$annotations\$raw\$spectral\$gnps,
output = get_params(step =
"prepare_annotations_gnps")\$files\$annotations\$prepared\$structural\$gnps,
str_stereo = get_params(step =
"prepare_annotations_gnps")\$files\$libraries\$sop\$merged\$structures\$stereo,
str_met = get_params(step =
"prepare_annotations_gnps")\$files\$libraries\$sop\$merged\$structures\$metadata,
str_tax_cla = get_params(step =
"prepare_annotations_gnps")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$cla,
str_tax_npc = get_params(step =
"prepare_annotations_gnps")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$npc
)
Arguments
input
|
character Character string or vector of paths to GNPS annotation files |
output
|
character Character string path for prepared GNPS annotations output |
str_stereo
|
character Character string path to structures stereochemistry file |
str_met
|
character Character string path to structures metadata file |
str_tax_cla
|
character Character string path to ClassyFire taxonomy file |
str_tax_npc
|
character Character string path to NPClassifier taxonomy file |
Value
Character string path to prepared GNPS annotations
See Also
Other preparation: prepare_annotations_mzmine(), prepare_annotations_mztab(), prepare_annotations_sirius(), prepare_annotations_spectra(), prepare_features_components(), prepare_features_edges(), prepare_features_tables(), 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_sop_pubchemlite(), prepare_libraries_spectra(), prepare_params(), prepare_taxa(), read_mztab()