technique | R Documentation |
Get and set methods for the AssignmentParameters
S4 class.
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
x |
S4 object of class |
value |
the value to set |
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()
.
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()
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