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Conversion to KPIC2 objects

Source: R/generics.R, R/features-kpic2.R
kpic2-conv.Rd

Converts a features object to an KPIC object.

Usage

getPICSet(obj, ...)

# S4 method for class 'features'
getPICSet(
  obj,
  loadRawData = TRUE,
  IMS = FALSE,
  EICParams = getDefEICParams(window = 0)
)

# S4 method for class 'featuresKPIC2'
getPICSet(obj, ...)

Arguments

obj

The features object that should be converted.

...

Ignored

loadRawData

Set to TRUE if analyses are available as mzXML or mzML files. Otherwise MS data is not loaded, and some dummy data (e.g. file paths) is used in the returned object.

IMS

(IMS workflow) Specifies which feature groups are considered for export in IMS workflows. The following options are valid:

  • "both": Selects IMS and non-IMS features.

  • "maybe": Selects non-IMS features and IMS features without assigned IMS precursor.

  • FALSE: Selects only non-IMS features.

  • TRUE: Selects only IMS features.

This should be kept FALSE as KPIC2 export currently does not support IMS features.

EICParams

A named list with parameters used for extracted ion chromatogram (EIC) creation. See the EIC parameters documentation for more details.

Details

The conversion process will introduce some dummy values for metadata not present in patRoon objects. If the features object was generated with KPIC2 and no post mobility assignment was performed, then no conversion is performed and the original KPIC2 object will be returned.

Use of raw HRMS data

The raw data interface of patRoon is used by getPICSet to process HRMS (or IMS-HRMS) data. Please see its documentation for more information on the supported formats and available configuration options.