sandy4321 / omicsmarker

automated 'omics' classification and feature selection

"OmicsMarkeR"

OmicsMarkeR is an R package that provides functions for classification and feature selection of 'omics' level datasets.

Motivation

During my studies as a developing Systems Biologist I discovered there were often varied techniques to answer the same initial question, how can I classify high-dimensional data (i.e. metabolomics, proteomics, transcriptomics)?
A second question usually posed in Biomarker investigations was which features are most important to such classification.

I initially pursued the repositories of CRAN and Bioconductor. I discovered such wonderful packages such as caret (which I highly recommend); however, I was unable to find a means of systematically running multiple algorithms in addition to stability metrics to provide confidence with features identified as important. This is critical as there seemed little practical benefit to classifying 2+ groups if the features identified varied between each test.

In my readings, I came upon an excellent chapter in the Lecture Notes of Computer Science Vol. 5212 entitled 'Robust Feature Selection Using Ensemble Feature Selection Techniques' by Yvan Sayes, Thomas Abeel, and Yves Van de Peer. From this chapter I decided to build this package, a tool to provide multiple multivariate classification and feature selection techniques complete with multiple stability metrics and aggregation techniques. In this manner, this package provides a way to systematically compare both data perturbation and function perturbation ensemble techniques complete with a harmonic mean of feature robustness and classification performance to evaluate the optimal model for the individual dataset. This following David Wolpert's 'No Free Lunch Theorem' as there is no single model that is appropriate for all problems.

I have made every effort to cite articles in which either the original technique was developed or applied. The interested reader, as well you should be, is highly encouraged to seek out these articles.

Installation

Stable version Bioconductor

source("http://bioconductor.org/biocLite.R")
biocLite("OmicsMarkeR")

Features in Progress

1. Access to fitted models (averaged or all bootstrapped results?)
2. Easy graphics access (scores/loadings plots, variable importance plots, etc.)
3. Summary graphics (across models)
4. Database searching (HMDB, MMCD, Metlin, LipidMaps, etc.)
5. Additional algorithms
6. Additional ensemble methods (bayesian, boosting, etc.)