parse.agilent

This package contains a couple of R functions for parsing the .csv output of Agilent’s MassHunter Qualitative software and returning the results as data frame.

Types of data

Both exported chromatogram files and exported spectra can be parsed. This includes extracted ion chromatograms (EICs), total ion chromatograms (TICs), base peak chromatograms (BPCs), extracted wavelength chromatograms (EWCs), total wavelength chromatograms (TWCs), instrument curves, etc.)

Requirements

1. R version 3.3 (untested on earlier versions)
2. tidyverse
3. data.table
4. devtools (for installation only)

Installation

library(devtools)
devtools::install_github('Stanford-ChEMH-MCAC/parse_agilent')

Use

library(parse.agilent)

# on chromatograms

cgrams.df <- parse_agilent_cgram_csv('PATH_TO_INSTALL/example_cgram_file.csv')
head(cgrams.df)

# on spectra
spectra.df <- parse_agilent_spectrum_csv()
head(spectra.df)