Spectral processing for profiling data — tar

Targets for spectral processing of profiling data.

Usage

tar_profiling(
  name,
  technique,
  mzML = NULL,
  sample_info = NULL,
  cls = "class",
  parameters = NULL,
  plots = c("chromatogram", "TIC"),
  summary = TRUE,
  export_path = "exports/spectral_processing"
)

Arguments

name: Symbol. The name for the collection of targets. This serves as a prefix for target names.
technique: The profiling technique to use. Should be one of the values returned by profilePro::availableTechniques().
mzML: A character vector of mzML data file paths. If NULL, target input will be expected from an existing target. See details.
sample_info: A tibble containing the sample information. See details for the specifications. If NULL, target input will be expected from an existing target. See details.
cls: Sample information column to use for plotting.
parameters: S4 object of class ProfileParameters. If NULL, default parameters for argument technique will be used.
plots: A character vector of plot types. Set to NULL to skip all plots.
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 processing mzML data files using profilePro.

Details

Specifying arguments mzML and sample_info as NULL enables the use of one of the data file and sample information from one of the input target factories, tar_input_file_path(), tar_input_grover() or tar_input_piggyback(). See the example using tar_input_piggyback() below.

Examples

if (FALSE) {
## Perform profiling processing by specifying the file paths and sample information directly
targets::tar_dir({
    targets::tar_script({
        library(hrmtargets)
        file_paths <- metaboData::filePaths('RP-UHPLC-HRMS','BdistachyonEcotypes',
                                            ask = FALSE)
        sample_info <- metaboData::runinfo('RP-UHPLC-HRMS','BdistachyonEcotypes',
                                           ask = FALSE)
        
        list(
            tar_profiling(example,
                          technique = 'LCMS-RP',
                          mzML = file_paths,
                          sample_info = sample_info)
        )
    })
    targets::tar_make()
    targets::tar_read(example_results_spectral_processing)
    targets::tar_read(example_plot_chromatogram)
})

## Perform spectral binning by using tar_input_piggyback() 
targets::tar_dir({
    targets::tar_script({
        name <- rlang::expr(example)
        library(hrmtargets)
        file_paths <- metaboData::filePaths('RP-UHPLC-HRMS','BdistachyonEcotypes',
                                            ask = FALSE)
        sample_info <- metaboData::runinfo('RP-UHPLC-HRMS','BdistachyonEcotypes',
                                           ask = FALSE)

        list(
            tar_input_file_path(!!name,
                                file_paths,
                                sample_info),
            tar_profiling(!!name,
                          'LCMS-RP')
        )
   })
   targets::tar_make()
   targets::tar_read(example_results_spectral_processing)
   targets::tar_read(example_plot_chromatogram)
})
}