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Get metabolomic data from MetaboLights database

Source: R/getMetaboLights.R
getMetaboLights.Rd

Get metabolomic data from MetaboLights database

Usage

getMetaboLights(study.id, output = "list", ...)

getMetaboLightsFile(study.id, file, ...)

Arguments

study.id

character vector specifying the study identifier of data that is going to be fetched from the MetaboLights database.

output

character scalar specifying output format. Must be "list", "TreeSE" (TreeSummarizedExperiment) or "SE" (SummarizedExperiment). (Default: "list")

...

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)

  • ion.mode Character scalar specifying metabolite assignment files to fetch. If "positive" only positive ions are fetched. Similarly "negative" means that negative ions are fetched if such data exists. By selecting "both", one can fetch both positive and negative ions. (Default: "both")

file

character vector specifying the files that are being fetched.

Value

list, SummarizedExperiment or TreeSummarizedExperiment

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.

See also

getResult getData

Examples


# This example is not run, because the server fails to respond sometimes.
if( FALSE ){
    res <- getMetaboLights("MTBLS4381")
    file_paths <- getMetaboLightsFile(
        study.id = "MTBLS4381",
        file = res[["assay_meta"]][["Raw Spectral Data File"]]
        )
    # Get data as SummarizedExperiment
    se <- getMetaboLights("MTBLS3540", output = "SE")
}