metaboData

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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.