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)