Molecular formula assignment — tar_mf

Targets for molecular formula assignment.

Usage

tar_mf_assignment(
  name,
  feature_data = NULL,
  parameters = assignments::assignmentParameters("FIE"),
  verbose = TRUE,
  summary = TRUE,
  export_path = "exports/molecular_formula_assignments"
)

Arguments

name: Symbol. The name for the collection of targets. This serves as a prefix for target names.
feature_data: A tibble containing a feature intensity matrix for which to assign molecular formulas. If NULL, target input will be expected from an existing target. See details.
parameters: S4 object of class AssignmentParameters.
verbose: Show assignment console output.
summary: Boolean. Include additional summary targets.
export_path: Destination path of export files. Set to NULL to skip exports.

Value

A list of target objects for molecular formula assignment.

Details

Specifying argument feature_data as NULL enables the use of input from the tar_pre_treatment() target factory, See the second example below.

Examples

if (FALSE) {
## Perform molecular formula assignment by specifying the feature data directly
targets::tar_dir({
    targets::tar_script({
        library(hrmtargets)
        
        list(
            tar_mf_assignment(assignments::feature_data)
        )
    })
    targets::tar_make()
    targets::tar_read(example_summary_assignments)
})

## Perform molecular formula assignment by using `tar_input_piggyback()`,
## `tar_input_spectral_binning()` and `tar_pre_treatment()` 
targets::tar_dir({
    targets::tar_script({
        library(hrmtargets)
        name <- rlang::expr(example)
        
        list(
            tar_input_piggyback(!!name,
                                'FIE-HRMS_BdistachyonTechnical',
                                repo = 'jasenfinch/metaboData'),
            tar_spectral_binning(!!name),
            tar_pre_treatment(!!name),
            tar_mf_assignment(!!name)
        )
    })
    targets::tar_make()
    targets::tar_read(example_results_spectral_processing)
    targets::tar_read(example_summary_assignments)
})
}