get_sample_data: get_sample_data

In robertyoung3/MSanalyzeNOM: Utilities for Analyzing Complex Natural Organic Matter (NOM) Mixtures After Formula Assignment

Description

This function reads sample Excel files exported by the MagLab's PetroOrg software after molecular formula (i.e., elemental composition) assignment, and returns a named list containing file and sample information, selected mass spectrometry parameters, mass spectrometry data for the assigned molecular formulas, mass spectrometry data for detected ions that could not be assigned molecular formulas ("no hits"), and a table of all detected ions.

Usage

get_sample_data(
  file = file.choose(),
  ion_technique = "NegESI",
  elements_used = c("C", "H", "N", "O", "S")
)

Arguments

file	a character string containing the filename and path for the Excel file created by PetroOrg after molecular formula assignment
ion_technique	a character string containing the MS ionization technique used (default = NegESI)
elements_used	a character vector containing the elements that were used for molecular formula assignments (default = C, H, N, O, S)

Details

This function was built for MS data from Fourier transform ion cyclotron resonance (FTICR) mass spectrometry using electrospray ionization in negative ion mode (NegESI). This is the default ion type. Because natural organic matter (NOM) is generally comprised primarily of the elements C, H, N, O, and S, they comprise the default elements used for molecular formula assignment.

If the form of the files exported by PetroOrg changes, this function will need to be revised.

Value

sample_data a named list containing 8 elements

robertyoung3/MSanalyzeNOM documentation built on June 7, 2021, 7:46 a.m.