Perform molecular formula assignment — assignMFs • assignments

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 or Analysis 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 or raw data on which to perform assignment when argument feature_data is of S4 class Analysis

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]