parameters: Parameter get and set methods

In jasenfinch/MFassign: Molecular Formula Assignment For High Resolution ESI-MS Based Metabolomics Data

Parameter get and set methods

Description

Get and set methods for the AssignmentParameters S4 class.

Usage

technique(x)

## S4 method for signature 'AssignmentParameters'
technique(x)

correlationsParameters(x)

## S4 method for signature 'AssignmentParameters'
correlationsParameters(x)

correlationsParameters(x) <- value

## S4 replacement method for signature 'AssignmentParameters,list'
correlationsParameters(x) <- value

limit(x)

## S4 method for signature 'AssignmentParameters'
limit(x)

limit(x) <- value

## S4 replacement method for signature 'AssignmentParameters'
limit(x) <- value

maxM(x)

## S4 method for signature 'AssignmentParameters'
maxM(x)

maxM(x) <- value

## S4 replacement method for signature 'AssignmentParameters'
maxM(x) <- value

MFrankThreshold(x)

## S4 method for signature 'AssignmentParameters'
MFrankThreshold(x)

MFrankThreshold(x) <- value

## S4 replacement method for signature 'AssignmentParameters'
MFrankThreshold(x) <- value

ppm(x)

## S4 method for signature 'AssignmentParameters'
ppm(x)

ppm(x) <- value

## S4 replacement method for signature 'AssignmentParameters'
ppm(x) <- value

isotopes(x)

## S4 method for signature 'AssignmentParameters'
isotopes(x)

isotopes(x) <- value

## S4 replacement method for signature 'AssignmentParameters'
isotopes(x) <- value

adducts(x)

## S4 method for signature 'AssignmentParameters'
adducts(x)

adducts(x) <- value

## S4 replacement method for signature 'AssignmentParameters'
adducts(x) <- value

transformations(x)

## S4 method for signature 'AssignmentParameters'
transformations(x)

transformations(x) <- value

## S4 replacement method for signature 'AssignmentParameters'
transformations(x) <- value

adductRules(x)

## S4 method for signature 'AssignmentParameters'
adductRules(x)

adductRules(x) <- value

## S4 replacement method for signature 'AssignmentParameters'
adductRules(x) <- value

isotopeRules(x)

## S4 method for signature 'AssignmentParameters'
isotopeRules(x)

isotopeRules(x) <- value

## S4 replacement method for signature 'AssignmentParameters'
isotopeRules(x) <- value

transformationRules(x)

## S4 method for signature 'AssignmentParameters'
transformationRules(x)

transformationRules(x) <- value

## S4 replacement method for signature 'AssignmentParameters'
transformationRules(x) <- value

Arguments

x	S4 object of class AssignmentParameters
value	the value to set

Details

• technique - Get the analytical technique.

• correlationsParameters - Get or set the correlation analysis parameters to be passed to metabolyseR::correlations().

• limit - Get or set the atomic mass unit limit for relationship calculation.

• maxM - Get or set the maximum molecular mass limit for which to assign molecular formulas.

• MFrankThreshold - Get or set the molecular formula rank threshold for molecular formula selection.

• ppm - Get or set the parts per million error threshold.

• isotopes - Get or set the isotope names. The order in which these are specified denotes the expected relative commonality within the data set.

• adducts - Get or set the adduct names for the ionisation modes. The order in which these are specified denotes the expected relative commonality within the data set for each ionisation mode.

• transformations - Get or set the transformation molecular formula changes.

• isotopeRules - Get or set the isotope rules table. The format of this tibble should match that of mzAnnotation::isotope_rules().

• adductRules - Get or set the adduct rules table. The format of this tibble should match that of mzAnnotation::adduct_rules().

• techniqueRules - Get or set the transformation rules table. The format of this tibble should match that of mzAnnotation::transformation_rules().

Examples

assignment_parameters <- assignmentParameters('FIE')

## Return the analytical technique
technique(assignment_parameters)

## Return correlations parameters
correlationsParameters(assignment_parameters)

## Set correlations parameters
correlationsParameters(assignment_parameters)$minCoef <- 0.75

## Return limit
limit(assignment_parameters)

## Set limit
limit(assignment_parameters) <- 0.002

## Return max M
maxM(assignment_parameters)

## Set max M
maxM(assignment_parameters) <- 500

## Return MF rank threshold
MFrankThreshold(assignment_parameters)

## Set MF rank threshold
MFrankThreshold(assignment_parameters) <- 3

## Return ppm
ppm(assignment_parameters)

## Set ppm
ppm(assignment_parameters) <- 3

## Return isotopes
isotopes(assignment_parameters)

## Set isotopes
isotopes(assignment_parameters) <- '13C'

## Return adducts
adducts(assignment_parameters)

## Set adducts
adducts(assignment_parameters) <- list(n = c('[M-H]1-','[M+Cl]1-'),
                                   p = c('[M+H]1+','[M+K]1+'))
                                   
## Return transformations
transformations(assignment_parameters)

## Set transformations
transformations(assignment_parameters) <- "M - [O] + [NH2]"

## Return adduct rules
adductRules(assignment_parameters)

## Set adduct rules
adductRules(assignment_parameters) <- mzAnnotation::adduct_rules()

## Return isotope rules
isotopeRules(assignment_parameters)

## Set isotope rules
isotopeRules(assignment_parameters) <- mzAnnotation::isotope_rules()

## Return transformation rules
transformationRules(assignment_parameters)

## Set transformation rules
transformationRules(assignment_parameters) <- mzAnnotation::transformation_rules()

jasenfinch/MFassign documentation built on Feb. 2, 2024, 11:21 a.m.