These functions use Metabolomics Workbench REST API to support data mining of publicly available lipidomics datasets.
list_mw_studies(keyword = "lipid")
fetch_mw_study(study_id)
read_mwTab(mwTab)
read_mw_datamatrix(file)A keyword to search for in Metabolomics Workbench studies.
The Metabolomics Workbench study ID.
File path or url for a mwTab file.
File path or url for the file containing the data matrix.
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.
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.
if (FALSE) {
list_mw_studies()
}
if (FALSE) {
fetch_mw_study("ST001111")
}