library("tima")
copy_backbone()
go_to_cache()
github <- "https://raw.githubusercontent.com/"
repo <- "taxonomicallyinformedannotation/tima-example-files/main/"
dir <- paste0(github, repo)
files <- get_params(step =
"prepare_libraries_sop_merged")$files$libraries$sop$prepared$lotus |>
gsub(pattern = ".gz", replacement = "", fixed = TRUE)
get_file(url = paste0(dir, files), export = files)
prepare_libraries_sop_merged(files = files)
unlink("data", recursive = TRUE)Prepare merged structure organism pairs libraries
Description
This function merges all structure-organism pair libraries (LOTUS, HMDB, ECMDB, etc.) into a single comprehensive library. Can optionally filter by taxonomic level to create biologically-focused subsets. Also splits structures into separate metadata tables.
Usage
prepare_libraries_sop_merged(
files = get_params(step = "prepare_libraries_sop_merged")\$files\$libraries\$sop\$prepared,
filter = get_params(step = "prepare_libraries_sop_merged")\$organisms\$filter\$mode,
level = get_params(step = "prepare_libraries_sop_merged")\$organisms\$filter\$level,
value = get_params(step = "prepare_libraries_sop_merged")\$organisms\$filter\$value,
cache = get_params(step =
"prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$processed,
npc_cache = get_params(step =
"prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$n,
cla_cache = get_params(step =
"prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$c,
output_key = get_params(step =
"prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$keys,
output_org_tax_ott = get_params(step =
"prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$organisms\$taxonomies\$ott,
output_str_can = get_params(step =
"prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$canonical,
output_str_stereo = get_params(step =
"prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$stereo,
output_str_met = get_params(step =
"prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$metadata,
output_str_tax_cla = get_params(step =
"prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$cla,
output_str_tax_npc = get_params(step =
"prepare_libraries_sop_merged")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$npc
)
Arguments
files
|
character Character vector or list of paths to prepared library files |
filter
|
logical Logical whether to filter the merged library by taxonomy |
level
|
character Character string taxonomic rank for filtering (kingdom, phylum, family, genus, etc.) |
value
|
character Character string taxon name(s) to keep (can use | for multiple, e.g., ‘Gentianaceae|Apocynaceae’) |
cache
|
character Character string path to cache directory for processed SMILES |
npc_cache
|
character Optional path to an additional NPClassifier taxonomy cache file (TSV/TSV.gz). Structures present in the merged library but missing NPClassifier taxonomy will be looked up in this cache. Expected columns: structure_smiles, structure_tax_npc_01pat, structure_tax_npc_02sup, structure_tax_npc_03cla. Alternative column names from external tools (e.g., pathway, superclass, class) are also supported.
|
cla_cache
|
character Optional path to an additional ClassyFire taxonomy cache file (TSV/TSV.gz). Structures present in the merged library but missing ClassyFire taxonomy will be looked up in this cache. Expected columns: structure_inchikey, structure_tax_cla_chemontid, structure_tax_cla_01kin, structure_tax_cla_02sup, structure_tax_cla_03cla, structure_tax_cla_04dirpar. Alternative column names (e.g., inchikey, chemontid, kingdom, superclass, class, directparent) are also supported.
|
output_key
|
character Character string path for output keys file |
output_org_tax_ott
|
character Character string path for organisms taxonomy (OTT) file |
output_str_can
|
character Character string path for structures canonical SMILES file |
output_str_stereo
|
character Character string path for structures stereochemistry file |
output_str_met
|
character Character string path for structures metadata file |
output_str_tax_cla
|
character Character string path for ClassyFire taxonomy file |
output_str_tax_npc
|
character Character string path for NPClassifier taxonomy file |
Details
Creates merged library by combining all available SOP sources, optionally filtering by taxonomic criteria (e.g., only Gentianaceae). Splits output into structures metadata, names, taxonomy, and organisms.
Value
Character string path to the prepared merged SOP library
See Also
Other preparation: prepare_annotations_gnps(), prepare_annotations_mzmine(), 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_spectra(), prepare_params(), prepare_taxa()