Molecular formula assignment methods — calcCorrelations • assignments

These methods provide access to performing the individual steps of the molecular formula assignment approach. See Details for more information of when it is best to use these instead of assignMFs().

Usage

calcCorrelations(assignment)

# S4 method for Assignment
calcCorrelations(assignment)

addIsoAssign(assignment)

# S4 method for Assignment
addIsoAssign(assignment)

transformationAssign(assignment)

# S4 method for Assignment
transformationAssign(assignment)

calcRelationships(assignment)

# S4 method for Assignment
calcRelationships(assignment)

Arguments

assignment: an object of S4 class Assignment

Value

An object of S4 class Assignment containing molecular formula assignments.

Details

In circumstances where the molecular formula assignment approach has high memory requirements, such as where there are many correlations (> 2 million) or many high m/z (>700), it may be preferable to perform the assignment steps separately as opposed to using assignMFs(). This can reduce the memory overheads required to successfully assign molecular formulas to the data and also enable the possibility of objects to be saved and/or unloaded between the assignment steps where needed.

Examples

plan(future::sequential)
p <- assignmentParameters('FIE-HRMS')

mf_assignments <- assignment(feature_data,p)

mf_assignments <- mf_assignments %>% 
   calcCorrelations() %>% 
   calcRelationships() %>% 
   addIsoAssign() %>% 
   transformationAssign()
#> Calculating correlations …

#> Calculating correlations 	✔ [10 correlations] [0.2S]
#> Calculating relationships …

#> Calculating relationships 	✔ [1.4S]
#> Adduct & isotopic assignment …
#> generating molecular formulas…

#> generating molecular formulas	✔ [8.2S]
#> 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]

mf_assignments
#> 
#> assignments v1.0.2 
#> Assignment: 
#> 	 Features:		 10 
#> 	 Correlations:		 10 
#> 	 Relationships:		 35 
#> 
#> 	 Adduct & isotope assignment: 
#> 		 Iterations:	 1 
#> 		 MFs:		 1 
#> 		 Assigned:	 5 
#> 
#> 	 Transformation assignment: 
#> 		 Iterations:	 1 
#> 		 MFs:		 1 
#> 		 Assigned:	 1 
#> 
#> 	 Total assignments:	 6 (60%) 
#> 	 Unique MFs:		 2 
#>