list_mw_studies {lipidr} | R Documentation

## Metabolomics Workbench integration

### Description

These functions use Metabolomics Workbench REST API to support data mining of publicly available lipidomics datasets.

### Usage

    list_mw_studies(keyword = "lipid")

    fetch_mw_study(study_id)

    read_mwTab(mwTab)

    read_mw_datamatrix(file)

### Arguments

`keyword` | A keyword to search for in Metabolomics Workbench studies.
`study_id` | The Metabolomics Workbench study ID.
`mwTab` | File path or url for a mwTab file.
`file` | File path or url for the file containing the data matrix.

### Value

`list_mw_studies` returns a data frame with studies matching the keyword. Study ID, title, author and details are retrieved.

All other functions return a LipidomicsExperiment object containing clinical and lipid intensity data.

### Functions

- `list_mw_studies`: retrieves a list of lipidomics studies from Metabolomics Workbench.

- `fetch_mw_study`: downloads and parse full data for a study from Metabolomics Workbench using a study ID. The function returns a LipidomicsExperiment where users can directly apply `lipidr` analysis workflow.

- `read_mwTab`: parses mwTab file into a LipidomicsExperiment.

- `read_mw_datamatrix`: parses a Metabolomics Workbench data matrix into a LipidomicsExperiment. Data matrix downloaded from Metabolomics Workbench are parsed into a LipidomicsExperiment object to enable `lipidr` workflow analysis.

### Examples

    ## Not run:
    list_mw_studies()

    ## End(Not run)
    ## Not run:
    fetch_mw_study("ST001111")

    ## End(Not run)

[Package lipidr version 2.0.0 Index]