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README.Rmd
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README.Rmd
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---
output:
md_document:
variant: markdown_github
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
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](https://zhuchcn.github.io/docs/packages/Metabase/intro/)
+ [Data input from WCMC report](https://zhuchcn.github.io/docs/packages/Metabase/lipidomics_wcmc/)
## 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