Parameter get and set methods
parameters.RdGet and set methods for the AssignmentParameters S4 class.
Usage
technique(x)
# S4 method for AssignmentParameters
technique(x)
correlationsParameters(x)
# S4 method for AssignmentParameters
correlationsParameters(x)
correlationsParameters(x) <- value
# S4 method for AssignmentParameters,list
correlationsParameters(x) <- value
limit(x)
# S4 method for AssignmentParameters
limit(x)
limit(x) <- value
# S4 method for AssignmentParameters
limit(x) <- value
maxM(x)
# S4 method for AssignmentParameters
maxM(x)
maxM(x) <- value
# S4 method for AssignmentParameters
maxM(x) <- value
MFrankThreshold(x)
# S4 method for AssignmentParameters
MFrankThreshold(x)
MFrankThreshold(x) <- value
# S4 method for AssignmentParameters
MFrankThreshold(x) <- value
ppm(x)
# S4 method for AssignmentParameters
ppm(x)
ppm(x) <- value
# S4 method for AssignmentParameters
ppm(x) <- value
isotopes(x)
# S4 method for AssignmentParameters
isotopes(x)
isotopes(x) <- value
# S4 method for AssignmentParameters
isotopes(x) <- value
adducts(x)
# S4 method for AssignmentParameters
adducts(x)
adducts(x) <- value
# S4 method for AssignmentParameters
adducts(x) <- value
transformations(x)
# S4 method for AssignmentParameters
transformations(x)
transformations(x) <- value
# S4 method for AssignmentParameters
transformations(x) <- value
adductRules(x)
# S4 method for AssignmentParameters
adductRules(x)
adductRules(x) <- value
# S4 method for AssignmentParameters
adductRules(x) <- value
isotopeRules(x)
# S4 method for AssignmentParameters
isotopeRules(x)
isotopeRules(x) <- value
# S4 method for AssignmentParameters
isotopeRules(x) <- value
transformationRules(x)
# S4 method for AssignmentParameters
transformationRules(x)
transformationRules(x) <- value
# S4 method for AssignmentParameters
transformationRules(x) <- valueDetails
technique- Get the analytical technique.correlationsParameters- Get or set the correlation analysis parameters to be passed tometabolyseR::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 ofmzAnnotation::isotope_rules().adductRules- Get or set the adduct rules table. The format of this tibble should match that ofmzAnnotation::adduct_rules().techniqueRules- Get or set the transformation rules table. The format of this tibble should match that ofmzAnnotation::transformation_rules().
Examples
assignment_parameters <- assignmentParameters('FIE')
## Return the analytical technique
technique(assignment_parameters)
#> [1] "FIE-HRMS"
## Return correlations parameters
correlationsParameters(assignment_parameters)
#> $method
#> [1] "spearman"
#>
#> $pAdjustMethod
#> [1] "bonferroni"
#>
#> $corPvalue
#> [1] 0.05
#>
#> $minCoef
#> [1] 0.7
#>
#> $maxCor
#> [1] Inf
#>
## Set correlations parameters
correlationsParameters(assignment_parameters)$minCoef <- 0.75
## Return limit
limit(assignment_parameters)
#> [1] 0.001
## Set limit
limit(assignment_parameters) <- 0.002
## Return max M
maxM(assignment_parameters)
#> [1] 800
## Set max M
maxM(assignment_parameters) <- 500
## Return MF rank threshold
MFrankThreshold(assignment_parameters)
#> [1] 3
## Set MF rank threshold
MFrankThreshold(assignment_parameters) <- 3
## Return ppm
ppm(assignment_parameters)
#> [1] 4
## Set ppm
ppm(assignment_parameters) <- 3
## Return isotopes
isotopes(assignment_parameters)
#> [1] "13C" "18O"
## Set isotopes
isotopes(assignment_parameters) <- '13C'
## Return adducts
adducts(assignment_parameters)
#> $n
#> [1] "[M-H]1-" "[M+Cl]1-" "[M+Cl37]1-" "[M+K-2H]1-" "[M-2H]2-"
#> [6] "[2M-H]1-"
#>
#> $p
#> [1] "[M+H]1+" "[M+K]1+" "[M+Na]1+" "[M+K41]1+" "[M+2H]2+" "[2M+H]1+"
#>
## 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)
#> [1] "M - [O] + [NH2]" "M - [OH] + [NH2]" "M + [H2]"
#> [4] "M - [H2] + [O]" "M - [H] + [CH3]" "M - [H] + [NH2]"
#> [7] "M - [H] + [OH]" "M + [H2O]" "M - [H3] + [H2O]"
#> [10] "M - [H] + [CHO2]" "M - [H] + [SO3]" "M - [H] + [PO3H2]"
## Set transformations
transformations(assignment_parameters) <- "M - [O] + [NH2]"
## Return adduct rules
adductRules(assignment_parameters)
#> # A tibble: 58 × 12
#> Name Charge xM Add Nelec AddAt RemAt AddEx RemEx Rule Default Isotopic
#> <chr> <int> <int> <dbl> <int> <chr> <chr> <chr> <chr> <chr> <int> <dbl>
#> 1 [M+3… 3 1 23.0 -3 NA NA Na3 NA HBA2… 0 0
#> 2 [M+H… 3 1 15.7 -3 NA NA Na2H NA HBA2… 0 0
#> 3 [M+2… 3 1 8.33 -3 NA NA NaH2 NA HBA2… 0 0
#> 4 [M+3… 3 1 1.01 -3 NA NA H3 NA HBA2… 0 0
#> 5 [2M+… 2 2 28.0 -2 NA NA H8O3 NA HBA2… 0 0
#> 6 [M+3… 2 1 62.5 -2 NA NA C6H1… NA HBA2… 0 0
#> 7 [M+2… 2 1 42.0 -2 NA NA C4H8… NA HBA2… 0 0
#> 8 [M+2… 2 1 23.0 -2 NA NA Na2 NA HBA2… 1 0
#> 9 [M+A… 2 1 21.5 -2 NA NA C2H5N NA HBA2… 0 0
#> 10 [M+H… 2 1 20.0 -2 NA NA KH NA HBA2… 1 0
#> # ℹ 48 more rows
## Set adduct rules
adductRules(assignment_parameters) <- mzAnnotation::adduct_rules()
## Return isotope rules
isotopeRules(assignment_parameters)
#> # A tibble: 8 × 4
#> Isotope `Mass Difference` Rule Default
#> <chr> <dbl> <chr> <int>
#> 1 13C 1.00 C>0 1
#> 2 13C2 2.01 C>1 1
#> 3 13C3 3.01 C>2 0
#> 4 13C4 4.01 C>3 0
#> 5 18O 2.00 O>0 1
#> 6 37Cl 2.00 Cl>0 0
#> 7 41K 2.00 K>0 0
#> 8 34S 2.00 S>0 1
## Set isotope rules
isotopeRules(assignment_parameters) <- mzAnnotation::isotope_rules()
## Return transformation rules
transformationRules(assignment_parameters)
#> # A tibble: 12 × 10
#> Name `MF Change` Difference C H N O P S Default
#> <chr> <chr> <dbl> <int> <int> <int> <int> <int> <int> <int>
#> 1 Transamin… M - [O] + … 0.0238 0 2 1 -1 0 0 1
#> 2 Ammonia l… M - [OH] +… -0.984 0 1 1 -1 0 0 1
#> 3 Hydrogena… M + [H2] 2.02 0 2 0 0 0 0 1
#> 4 Alcohol t… M - [H2] +… 14.0 0 -2 0 1 0 0 1
#> 5 Methylati… M - [H] + … 14.0 1 2 0 0 0 0 1
#> 6 Transamin… M - [H] + … 15.0 0 1 1 0 0 0 1
#> 7 Hydroxyla… M - [H] + … 16.0 0 0 0 1 0 0 1
#> 8 Hydration M + [H2O] 18.0 0 2 0 1 0 0 1
#> 9 Methyl to… M - [H3] +… 30.0 0 -1 0 1 0 0 1
#> 10 Carboxyla… M - [H] + … 44.0 1 0 0 2 0 0 1
#> 11 Sulphation M - [H] + … 80.0 0 -1 0 3 0 1 1
#> 12 Phosphory… M - [H] + … 80.0 0 1 0 3 1 0 1
## Set transformation rules
transformationRules(assignment_parameters) <- mzAnnotation::transformation_rules()