metaboData

Jasen Finch

metaboData provides raw and processed example metabolomics data sets. This document concisely outlines how to access the data sets and the meta information provided.

Accessing data sets

Load the library:

library(metaboData)

The example data sets are stored remotely in the releases of the GitHub repository and accessed using the piggyback package. The available data sets can be viewed using:

availableDataSets()

The available metabolomic techniques can be returned using:

techniques()

The available data sets for a given metabolomic technique can be returned using:

dataSets(techniques()[1])

A particular data set can be downloaded for use with:

downloadDataSet(techniques()[1],
                dataSets()[1])

By default these will be stored within the library location. This behaviour can be adjusted using the dataSetDir and internalDir arguments.

File paths for data files within a given data set can be returned using the following:

files <- filePaths(
    techniques()[1],
    dataSets(techniques()[1])[1])

An experimental description can be retrieved for a given experiment of a given metabolomic technique using:

experimentDescription <- description(
   techniques()[1],
   dataSets(techniques()[1])[1])

Run information can be retrieved for a given experiment of a given metabolomic technique using:

info <- runinfo(
    techniques()[1],
    dataSets(techniques()[1])[1])

head(info)

For filePaths, description and runinfo, if the specified data set is not available locally, by default the user will be prompted to consent to downloading the data. The ask = FALSE argument can be used to override this behaviour.

The abr1 FIE-MS data set from the FIEmspro package is also available via lazy-load.