library("tima")
copy_backbone()
go_to_cache()
github <- "https://raw.githubusercontent.com/"
repo <- "taxonomicallyinformedannotation/tima-example-files/main/"
data_interim <- "data/interim/"
dir <- paste0(github, repo)
dir <- paste0(dir, data_interim)
dir_sop_mer <- paste0(dir, "libraries/sop/merged/")
dir_str <- paste0(dir_sop_mer, "structures/")
dir_tax <- paste0(dir_str, "taxonomies/")
annotate_masses(
features = paste0(dir, "features/example_features.tsv"),
library = paste0(dir_sop_mer, "keys.tsv"),
str_stereo = paste0(dir_str, "stereo.tsv"),
str_met = paste0(dir_str, "metadata.tsv"),
str_nam = paste0(dir_str, "names.tsv"),
str_tax_cla = paste0(dir_tax, "classyfire.tsv"),
str_tax_npc = paste0(dir_tax, "npc.tsv")
)
unlink("data", recursive = TRUE)Annotate masses
Description
This function annotates a feature table based on exact mass match. It requires a structural library, its metadata, and lists of adducts, clusters, and neutral losses to be considered. The polarity has to be pos or neg and retention time and mass tolerances should be given. The feature table is expected to be pre-formatted.
Usage
annotate_masses(
features = get_params(step = "annotate_masses")\$files\$features\$prepared,
output_annotations = get_params(step =
"annotate_masses")\$files\$annotations\$prepared\$structural\$ms1,
output_edges = get_params(step = "annotate_masses")\$files\$networks\$spectral\$edges\$raw,
name_source = get_params(step = "annotate_masses")\$names\$source,
name_target = get_params(step = "annotate_masses")\$names\$target,
library = get_params(step = "annotate_masses")\$files\$libraries\$sop\$merged\$keys,
str_stereo = get_params(step =
"annotate_masses")\$files\$libraries\$sop\$merged\$structures\$stereo,
str_met = get_params(step =
"annotate_masses")\$files\$libraries\$sop\$merged\$structures\$metadata,
str_nam = get_params(step =
"annotate_masses")\$files\$libraries\$sop\$merged\$structures\$names,
str_tax_cla = get_params(step =
"annotate_masses")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$cla,
str_tax_npc = get_params(step =
"annotate_masses")\$files\$libraries\$sop\$merged\$structures\$taxonomies\$npc,
adducts_list = get_params(step = "annotate_masses")\$ms\$adducts,
clusters_list = get_params(step = "annotate_masses")\$ms\$clusters,
neutral_losses_list = get_params(step = "annotate_masses")\$ms\$neutral_losses,
ms_mode = get_params(step = "annotate_masses")\$ms\$polarity,
tolerance_ppm = get_params(step = "annotate_masses")\$ms\$tolerances\$mass\$ppm\$ms1,
tolerance_rt = get_params(step = "annotate_masses")\$ms\$tolerances\$rt\$adducts
)
Arguments
features
|
Table containing your previous annotation to complement |
output_annotations
|
Output for mass based structural annotations |
output_edges
|
Output for mass based edges |
name_source
|
Name of the source features column |
name_target
|
Name of the target features column |
library
|
Library containing the keys |
str_stereo
|
File containing structures stereo |
str_met
|
File containing structures metadata |
str_nam
|
File containing structures names |
str_tax_cla
|
File containing Classyfire taxonomy |
str_tax_npc
|
File containing NPClassifier taxonomy |
adducts_list
|
List of adducts to be used |
clusters_list
|
List of clusters to be used |
neutral_losses_list
|
List of neutral losses to be used |
ms_mode
|
Ionization mode. Must be ‘pos’ or ‘neg’ |
tolerance_ppm
|
Tolerance to perform annotation. Should be <= 20 ppm |
tolerance_rt
|
Tolerance to group adducts. Should be <= 0.05 minutes |
Value
The path to the files containing MS1 annotations and edges