metaboData provides raw and processed example metabolomics data sets. This document concisely outlines how to access the data sets and the meta information provided.
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:
<- filePaths(
files techniques()[1],
dataSets(techniques()[1])[1])
An experimental description can be retrieved for a given experiment of a given metabolomic technique using:
<- description(
experimentDescription techniques()[1],
dataSets(techniques()[1])[1])
Run information can be retrieved for a given experiment of a given metabolomic technique using:
<- runinfo(
info 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.