prepare_libraries_sop_merged: Prepare merged structure organism pairs libraries

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

Prepare merged structure organism pairs libraries

Description

This function prepares the libraries made of all sub-libraries containing structure-organism pairs

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$value,
  output_key = get_params(step =
    "prepare_libraries_sop_merged")$files$libraries$sop$merged$keys,
  output_org_tax_ott = get_params(step =
    "prepare_libraries_sop_merged")$files$libraries$sop$merged$organisms$taxonomies$ott,
  output_str_stereo = get_params(step =
    "prepare_libraries_sop_merged")$files$libraries$sop$merged$structures$stereo,
  output_str_met = get_params(step =
    "prepare_libraries_sop_merged")$files$libraries$sop$merged$structures$metadata,
  output_str_nam = get_params(step =
    "prepare_libraries_sop_merged")$files$libraries$sop$merged$structures$names,
  output_str_tax_cla = get_params(step =
    "prepare_libraries_sop_merged")$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	List of libraries to be merged
filter	Boolean. TRUE or FALSE if you want to filter the library
level	Biological rank to be filtered. Kingdom, phylum, family, genus, ...
value	Name of the taxon or taxa to be kept, e.g. 'Gentianaceae|Apocynaceae'
output_key	Output file for keys
output_org_tax_ott	Output file for organisms taxonomy (OTT)
output_str_stereo	Output file for structures stereo
output_str_met	Output file for structures metadata
output_str_nam	Output file for structures names
output_str_tax_cla	Output file for structures taxonomy (Classyfire)
output_str_tax_npc	Output file for structures taxonomy (NPC)

Details

It can be restricted to specific taxa to have more biologically meaningful annotation.

Value

The path to the prepared structure-organism pairs library MERGED

Examples

## Not run: 
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)

## End(Not run)

taxonomicallyinformedannotation/tima-r documentation built on Nov. 20, 2024, 4:34 a.m.