Skip to content

OmicsARules: a R package for integration of multi-omics datasets via association rules mining

0Citations
Citations of this article
41Readers
Mendeley users who have this article in their library.

This artice is free to access.

Abstract

Background: The improvements of high throughput technologies have produced large amounts of multi-omics experiments datasets. Initial analysis of these data has revealed many concurrent gene alterations within single dataset or/and among multiple omics datasets. Although powerful bioinformatics pipelines have been developed to store, manipulate and analyze these data, few explicitly find and assess the recurrent co-occurring aberrations across multiple regulation levels. Results: Here, we introduced a novel R-package (called OmicsARules) to identify the concerted changes among genes under association rules mining framework. OmicsARules embedded a new rule-interestingness measure, Lamda3, to evaluate the associated pattern and prioritize the most biologically meaningful gene associations. As demonstrated with DNA methlylation and RNA-seq datasets from breast invasive carcinoma (BRCA), esophageal carcinoma (ESCA) and lung adenocarcinoma (LUAD), Lamda3 achieved better biological significance over other rule-ranking measures. Furthermore, OmicsARules can illustrate the mechanistic connections between methlylation and transcription, based on combined omics dataset. OmicsARules is available as a free and open-source R package. Conclusions: OmicsARules searches for concurrent patterns among frequently altered genes, thus provides a new dimension for exploring single or multiple omics data across sequencing platforms.

Cite

CITATION STYLE

APA

Chen, D., Zhang, F., Zhao, Q., & Xu, J. (2019). OmicsARules: a R package for integration of multi-omics datasets via association rules mining. BMC Bioinformatics, 20(1). https://doi.org/10.1186/s12859-019-3171-0

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free