Perform molecular formula assignment
assign.Rd
Perform automated molecular formula assignment.
Usage
assignMFs(
feature_data,
parameters = assignmentParameters("FIE-HRMS"),
verbose = TRUE,
...
)
# S4 method for tbl_df
assignMFs(
feature_data,
parameters = assignmentParameters("FIE-HRMS"),
verbose = TRUE
)
# S4 method for AnalysisData
assignMFs(
feature_data,
parameters = assignmentParameters("FIE"),
verbose = TRUE
)
# S4 method for Analysis
assignMFs(
feature_data,
parameters = assignmentParameters("FIE"),
verbose = TRUE,
type = c("pre-treated", "raw")
)
Arguments
- feature_data
a tibble or an object of S4 class
AnalysisData
orAnalysis
containing the feature intensity matrix of m/z for which to assign molecular formulas. See details.- parameters
an S4 object of class
AssignmentParamters
containing the parameters for molecular formula assignment- verbose
should progress output be printed to the console
- ...
arguments to pass to the relevant method
- type
pre-treated
orraw
data on which to perform assignment when argumentfeature_data
is of S4 classAnalysis
Details
If argument feature_data
is specified as a tibble, this should be a feature intensity matrix where
the columns are the m/z
features to assign and the rows are the individual observations, with the
cells as abundance values. he m/z features provided as column names should be in the form of
<ionisation_mode><m/z>@<retention_time>. Ionisation mode should be given as a prefix n or p for negative
or positive ionisation modes respectively. Feature m/z should be provided to an accuracy of least 5 decimal
places. The retention time portion (@<retention_time>) is only required for LC-MS data and should be provided
in minutes.
Examples
plan(future::sequential)
p <- assignmentParameters('FIE-HRMS')
assignments <- assignMFs(feature_data,p)
#>
#> assignments v1.0.2 Thu Jan 11 15:07:08 2024
#> ________________________________________________________________________________
#> Assignment Parameters:
#>
#> Technique: FIE-HRMS
#> Max M: 800
#> MF rank threshold: 3
#> PPM threshold: 4
#> Relationship limit: 0.001
#> RT limit:
#> Correlations:
#> method: spearman
#> pAdjustMethod: bonferroni
#> corPvalue: 0.05
#> minCoef: 0.7
#> maxCor: Inf
#>
#> Adducts:
#> n: [M-H]1-, [M+Cl]1-, [M+Cl37]1-, [M+K-2H]1-, [M-2H]2-, [2M-H]1-
#> p: [M+H]1+, [M+K]1+, [M+Na]1+, [M+K41]1+, [M+2H]2+, [2M+H]1+
#> Isotopes: 13C, 18O
#> Transformations: M - [O] + [NH2], M - [OH] + [NH2], M + [H2], M - [H2] + [O], M - [H] + [CH3], M - [H] + [NH2], M - [H] + [OH], M + [H2O], M - [H3] + [H2O], M - [H] + [CHO2], M - [H] + [SO3], M - [H] + [PO3H2]
#> ________________________________________________________________________________
#> No. m/z: 10
#> Calculating correlations …
#> Calculating correlations ✔ [10 correlations] [0.2S]
#> Calculating relationships …
#> Calculating relationships ✔ [1.7S]
#> Adduct & isotopic assignment …
#> generating molecular formulas…
#> generating molecular formulas ✔ [8.3S]
#> iteration 1…
#> iteration 1 ✔ [0.4S]
#> iteration 2…
#> Adduct & isotopic assignment ✔ [9.3S]
#> Transformation assignment…
#> iteration 1 …
#> iteration 1 ✔ [1.2S]
#> iteration 2 …
#> Transformation assignment ✔ [1.2S]
#> ________________________________________________________________________________
#>
#> Complete! [12.8S]