mSet-class: A virtual S4 class to store an quantitative experiment data.

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

Description

This is a virtual S4 class to store the entire dataset from a quantitative experiment, such as metabolomics and proteomics experiments.

This is a virtual class so it can only be inherited from, but not be constructed directly. You can either use the classes the inherits this class defined by this package, or you can define your own class and inherits it to use some of its features.

The classes that inherits from the virtual mSet class are: the MetabolomicsSet-class and the ProteomicsSet-class .

The mSet class and all the classes that inherits from it should contain at least the four slots that were discussed below.

Slots

conc_table

A conc_table-class object that stores the concentration information from the experiment. The column names should be the feature IDs, and the rownames should be the row IDs. This should be a numeric matrix.

sample_table

A sample_table-class object that stores the sample meta-data information. The row names should be sample IDs and should match the column names of the conc_table.

feature_data

A feature_data-class object that stores the feature infromation during the experiment. The row names should be feature IDs and should match the row names of the conc_table.

experiment_data

A list contains additional untabular experimental data

Author(s)

Chenghao Zhu

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