In zhuchcn/Metabase: Data container, handling, and visualization for high through-put quantitative experiment data.

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

Metabase

Description

This is a R package that provides a solution to handle data from quantitative experiments such as metabolomics and proteomics. It aims to reduce the data analysis workload, simplify tedious and repeating steps during data cleaning, transforming, summarizing and visualizing, and help researchers to analyze and explore their data easily. It uses R's S4 object oriented programing system, inspired by the bioconductor R package Biobase and phyloseq for sequencing data.

The virtual super class mSet is the base of this package. It has 4 slots, a conc_table slot that contains the numeric concentration values for each sample and feature, a sample_table slot that contains all the sample metadata, a feature_data slot contains all the feature information from the experiment, and a experiment_data slot that contains all the additional experiment information. The mSet is a virtual class so it ca n not be constructed directly. There are several classes that inherit from it, MetabolomicsSet, LipidomicsSet, GlycomicsSet, MicrobiomeSet, and MultxSet. They do not have huge differences in terms of the design.

Vignettes

• Introduction to Metabase
• Data input from WCMC report

To do:

• [x] The ExperimentData-class is currently too strict. The structure should be more flexible to handle different study type.
• [ ] Make it compatible with xcms

zhuchcn/Metabase documentation built on July 23, 2019, 1:36 p.m.