fioRa (version 0.3.7)

read_fiora: Read a fiora result file (mgf) into a R object.

Description

Allows to import a `fioRa` output file (msp like format) to a list like format or simplified to a data frame or Spectra object.

Usage

read_fiora(fl, fmt = c("list", "df", "Spectra"))

Value

A result list of length = n_compounds containing metadata fields as sub-lists and the predicted MS^2 spectrum as sub-list `spec`. You can set parameter `fmt` to 'df' in which case each compound list will be coerced to a data frame row (spectra will be encoded as 'mz1:int1 mz2:int2 ...' and information regarding SMILES, adduct or formula per peak will be lost).

Arguments

fl

file.

fmt

A named list object is returned if not specified otherwise. Set 'fmt=df' to simplify the return value to a data frame. Use 'fmt=Spectra' to convert to a [Spectra::Spectra()] object.

See Also

[Spectra::Spectra()]

Examples

fl <- system.file("extdata/annotated_output.mgf", package = "fioRa")

# read as data.frame (return a simplified version)
str(fioRa::read_fiora(fl = fl, fmt = "df"))

# \donttest{
  # read as a list (standard case)
  fioRa::read_fiora(fl = fl)

  # read as Spectra object (requires Spectra-package)
  if (requireNamespace("Spectra", quietly = TRUE)) {
    fioRa::read_fiora(fl = fl, fmt = "Spectra")
   }
# }