clean_chemo: Clean chemo

In taxonomicallyinformedannotation/tima-r: Taxonomically Informed Metabolite Annotation

Clean chemo

Description

This function cleans the results obtained after chemical weighting

Usage

clean_chemo(
  annot_table_wei_chemo = get("annot_table_wei_chemo", envir = parent.frame()),
  components_table = get("components_table", envir = parent.frame()),
  features_table = get("features_table", envir = parent.frame()),
  structure_organism_pairs_table = get("structure_organism_pairs_table", envir =
    parent.frame()),
  candidates_final = get("candidates_final", envir = parent.frame()),
  minimal_ms1_bio = get("minimal_ms1_bio", envir = parent.frame()),
  minimal_ms1_chemo = get("minimal_ms1_chemo", envir = parent.frame()),
  minimal_ms1_condition = get("minimal_ms1_condition", envir = parent.frame()),
  high_confidence = get("high_confidence", envir = parent.frame()),
  remove_ties = get("remove_ties", envir = parent.frame()),
  summarise = get("summarise", envir = parent.frame())
)

Arguments

annot_table_wei_chemo	Table containing your chemically weighted annotation
components_table	Prepared components file
features_table	Prepared features file
structure_organism_pairs_table	Table containing the structure - organism pairs
candidates_final	Number of final candidates to keep
minimal_ms1_bio	Minimal biological score to keep MS1 based annotation
minimal_ms1_chemo	Minimal chemical score to keep MS1 based annotation
minimal_ms1_condition	Condition to be used. Must be "OR" or "AND".
high_confidence	Report high confidence candidates only. BOOLEAN
remove_ties	Remove ties. BOOLEAN
summarise	Boolean. summarise results (1 row per feature)

Value

A table containing the chemically weighted annotation where only a given number of initial candidates are kept

See Also

weight_chemo

Examples

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taxonomicallyinformedannotation/tima-r documentation built on Nov. 24, 2024, 9:34 p.m.