This function annotates masses
Usage
annotate_masses(
features = get_params(step = "annotate_masses")$files$features$prepared,
filter_nitro = get_params(step = "annotate_masses")$options$nitrogen_rule,
output_annotations = get_params(step =
"annotate_masses")$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$minutes
)Arguments
- features
Table containing your previous annotation to complement
- filter_nitro
Filter according to Nitrogen rule. Boolean
- 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 <= 10 ppm
- tolerance_rt
Tolerance to group adducts. Should be <= 0.1min
- adducts_masses_list
Adducts masses
- clusters_neg
Negative clusters to be used
- clusters_pos
Positive clusters to be used