Get metabolomic data from MetaboLights database
Arguments
- study.id
character vector
specifying the study identifier of data that is going to be fetched from the MetaboLights database.- ...
optional arguments:
cache.dir
Character scalar
specifying directory where downloaded file is stored. (Default:tempdir()
)timeout
Integer scalar
specifying timeout in seconds for loading a file. (Default:5*60
)
- file
character vector
specifying the files that are being fetched.
Details
The HoloFood database primarily comprises targeted metabolomic data,
omitting non-targeted metabolomic information. Nonetheless, it features URLs
linking to studies within the MetaboLights database. This functionality
enables users to access non-targeted metabolomic data. The
getMetaboLights
function returns
a structured list encompassing processed data in data.frame
format
for study metadata, assay metadata, and assay.
The metadata includes the file names of spectra data. Those files can be
loaded with getMetaboLightsFile
. Alternatively, once you've identified
the study and files to fetch, you can refer to this
[vignette](https://rformassspectrometry.github.io/MsIO/articles/MsIO.html#loading-data-from-metabolights)
for instructions on loading the data directly into an MsExperiment
object, specifically designed for metabolomics spectra data.