mw: Metabolomics Workbench integration

In ahmohamed/lipidr: Data Mining and Analysis of Lipidomics Datasets

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)

ahmohamed/lipidr documentation built on July 7, 2023, 2:22 a.m.