Import Data into Sirius

Usage

import(
  sirius,
  spectra,
  ms_column_name = character(),
  adducts = character(),
  chunkSize = 500,
  deleteExistingFeatures = TRUE
)

Arguments

sirius: Sirius. The connection to the Sirius instance with a loaded project.
spectra: Spectra object containing MS data to import. Can contain MS1 and/or MS2 spectra. If multiple MS levels are present, the ms_column_name parameter must be provided to group spectra into features. See the fragmentGroupIndex() function from the Spectra package for generating appropriate grouping indices.
ms_column_name: character(1). This is the name of a column expected in the spectraData of the input spectra object. MS1 and MS2 spectra with the same index in this column will be grouped into a single feature. This parameter must be provided if the object has multiple msLevels. If no column name is provided and the object contains only one MS level, then each MS1 spectrum will be exported as a separate feature in Sirius. Lastly, we support multiple MS2 spectra per feature, but only one MS1 spectrum per index. Please merge MS1 spectra beforehand if necessary.
adducts: character vector of the adduct(s) associated with the features being imported. Must be either length 1 or the same length as the number of features. If of length 1 and fewer than the number of features, the same adduct will be used for all features.
chunkSize: numeric(1). Number of features to process and import at once. Importing can be slow, so this is useful when working with a very large number of spectra.
deleteExistingFeatures: logical(1). If TRUE, all existing features will be deleted before importing the new ones.