mf | R Documentation |
Consensus
and Construction
S4 classesAccessor methods for the Consensus
and Construction
S4 classes.
mf(x)
## S4 method for signature 'Consensus'
mf(x)
adductRules(x)
## S4 method for signature 'Consensus'
adductRules(x)
organism(x)
## S4 method for signature 'Consensus'
organism(x)
database(x)
## S4 method for signature 'Consensus'
database(x)
hits(x)
## S4 method for signature 'Consensus'
hits(x)
PIPs(x)
## S4 method for signature 'Consensus'
PIPs(x)
classifications(x)
## S4 method for signature 'Consensus'
classifications(x)
consensusClassifications(x)
## S4 method for signature 'Consensus'
consensusClassifications(x)
consensus(x, adduct, threshold = 66)
## S4 method for signature 'Consensus'
consensus(x, adduct, threshold = 66)
## S4 method for signature 'Construction'
classifications(x)
summariseClassifications(x)
## S4 method for signature 'Construction'
summariseClassifications(x)
x |
object of S4 class |
adduct |
the ionisation adduct for which a consensus should be calculated |
threshold |
the percentage majority threshold for consensus classification |
mf
- Return the searched molecular formula
adductRules
- Return a tibble of adduct formation rules.
organism
- Return the KEGG organism ID.
database
- Return the searched database.
threshold
- Return the percentage consensus threshold for structural classification selection.
hits
- Return a MetaboliteDatabase
ionisation database of matched database hits.
PIPs
- Return the putative ionisation products of database hits
classifications
-Return the structural chemical classifications of database hits.
consensusClassifications
- Return the consensus classification or classifications.
summariseClassifications
- Return a tibble of summarised consensus structural classifications.
A character, a numeric, a tibble or an object of S4 class MetaboliteDatabase
, depending on the method used.
consensus <- construct(
'C4H6O5',
organism = 'hsa')
## Return the molecular formula
mf(consensus)
## Return the adduct formation rules
adductRules(consensus)
## Return the KEGG organism ID
organism(consensus)
## Return the searched database
database(consensus)
## Return the `MetaboliteDatabase` ionisation database of searched database hits
hits(consensus)
## Return the putative ionisation products
PIPs(consensus)
## Return the structural classifications
classifications(consensus)
## Return the consensus structural classification
consensusClassifications(consensus)
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