access: Accessor methods for the 'Consensus' and 'Construction' S4...

In jasenfinch/consensus: Consensus Structural Chemical Classifications for Putative Molecular Formula Assignments

Accessor methods for the Consensus and Construction S4 classes

Description

Accessor methods for the Consensus and Construction S4 classes.

Usage

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)

Arguments

x	object of S4 class Consensus or Construction
adduct	the ionisation adduct for which a consensus should be calculated
threshold	the percentage majority threshold for consensus classification

Details

• 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.

Value

A character, a numeric, a tibble or an object of S4 class MetaboliteDatabase, depending on the method used.

Examples

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)

jasenfinch/consensus documentation built on Sept. 2, 2023, 8:13 a.m.