In wilsontom/golmDB: Parse the Golm database

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Introduction

The Golm Metabolome Database is a collection of reference mass spectra from biologically active metabolites that have been quantified using Gas Chromatography (GC) Mass Spectrometry (MS). The golmDB package provides a simple method to parse the Golm database, so it can be easily used in downstream processing pipelines.

Installation

golmDB can be installed directly from GitHub using the remotes package.

remotes::install_github('wilsontom/golmDB')

Creating a golmDB object

Before creating a new golmDB object, you first need to download the version of Golm that you require. All the different Golm database files can be downloaded here. golmDB requires the database to be downloaded in the MSP format.

Once you have the Golm database file, you can create a new golmDB object by using the openGolmDB function with the path of the database file.

library(golmDB)

GolmDB_MDN35 <-
  openGolmDB('../inst/extdata/GMD_20111121_MDN35_FAME_MSP.txt')

GolmDB_MDN35

golmDB utilises two separate S4 classes. The GolmDB class contains the entire database; where each database accession is stored in it's own GolmAccession class. The GolmDB accession slot, is large list of GolmAccession objects.

slotNames(GolmDB_MDN35)

length(GolmDB_MDN35@accessions)

GolmDB_MDN35@accessions[[1]]

Search Database

The searchDB method can be used to create smaller database objects, based on the results of searching for a particular pattern. For example, if you are only interested in Fatty Acid Methyl Esters then you can use 'methyl esters' as a search pattern.

GolmDB_FAME <- searchDB(GolmDB_MDN35, pattern = 'methyl ester')

GolmDB_FAME

wilsontom/golmDB documentation built on March 6, 2021, 12:29 a.m.