accessors: Assignment accessors

In jasenfinch/MFassign: Molecular Formula Assignment For High Resolution ESI-MS Based Metabolomics Data

Assignment accessors

Description

Access methods for Assignment S4 class

Usage

featureData(assignment)

## S4 method for signature 'Assignment'
featureData(assignment)

correlations(assignment)

## S4 method for signature 'Assignment'
correlations(assignment)

relationships(assignment)

## S4 method for signature 'Assignment'
relationships(assignment)

iterations(assignment)

## S4 method for signature 'Assignment'
iterations(assignment)

graph(assignment, iteration, type = c("selected", "all"))

## S4 method for signature 'Assignment'
graph(assignment, iteration, type = c("selected", "all"))

components(assignment, iteration, type = c("selected", "all"))

## S4 method for signature 'Assignment'
components(assignment, iteration, type = c("selected", "all"))

featureComponents(assignment, feature, type = c("selected", "all"))

## S4 method for signature 'Assignment'
featureComponents(assignment, feature, type = c("selected", "all"))

component(assignment, component, iteration, type = c("selected", "all"))

## S4 method for signature 'Assignment'
component(assignment, component, iteration, type = c("selected", "all"))

assignments(assignment)

## S4 method for signature 'Assignment'
assignments(assignment)

assignedData(assignment)

## S4 method for signature 'Assignment'
assignedData(assignment)

summariseAssignments(assignment)

## S4 method for signature 'Assignment'
summariseAssignments(assignment)

Arguments

assignment	S4 object of class Assignment
iteration	the assignment iteration
type	the graph type to return. filtered returns the assignment graph after component selection. all returns all assignment components.
feature	feature information to extract
component	component number to extract

Details

• featureData - Return the initially specifed m/z feature data.

• correlations - Return the correlation analysis results.

• relationships - Return the calculated relationships.

• iterations - Return the assignment iteration performed.

• graph - Return a selected graph.

• components - Return the component information for an assignment iteration.

• featureComponents - Return the component information for a selected feature.

• component - Extract a component graph.

• assignments - Return the molecular formulas assigned to the m/z features.

• assignedData - Return the m/z peak intensity matrix with the molecular formula assignments included in the column names.

• summariseAssignments - Return a tibble of the assignments summarised by molecular formula.

Value

A tibble or tbl_graph containing assignment results depending on the method used.

Examples

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

mf_assignments <- assignMFs(feature_data,p)

## Return feature data
featureData(mf_assignments)

## Return correlations
correlations(mf_assignments)

## Return relationships
relationships(mf_assignments)

## Return the available iterations
iterations(mf_assignments)

## Return a selected graph
graph(mf_assignments,'A&I1')

## Return a component information for a selected graph
components(mf_assignments,'A&I1')

## Return a component information for a selected feature
featureComponents(mf_assignments,'n191.01962')

 ## Extract a component graph
component(mf_assignments,1,'A&I1')

## Return assignments
assignments(mf_assignments)

## Return an m/z intensity matrix with the assignments included
## in the column names
assignedData(mf_assignments)

## Return the assignments summarised by molecular formula
summariseAssignments(mf_assignments)

jasenfinch/MFassign documentation built on Feb. 2, 2024, 11:21 a.m.