An R package for divergence analysis of omics data.

TitleAn R package for divergence analysis of omics data.
Publication TypeJournal Article
Year of Publication2021
AuthorsDinalankara W, Ke Q, Geman D, Marchionni L
JournalPLoS One
Volume16
Issue4
Paginatione0249002
Date Published2021
ISSN1932-6203
KeywordsDatabases, Genetic, Genomics, Humans, Neoplasms, Software
Abstract

Given the ever-increasing amount of high-dimensional and complex omics data becoming available, it is increasingly important to discover simple but effective methods of analysis. Divergence analysis transforms each entry of a high-dimensional omics profile into a digitized (binary or ternary) code based on the deviation of the entry from a given baseline population. This is a novel framework that is significantly different from existing omics data analysis methods: it allows digitization of continuous omics data at the univariate or multivariate level, facilitates sample level analysis, and is applicable on many different omics platforms. The divergence package, available on the R platform through the Bioconductor repository collection, provides easy-to-use functions for carrying out this transformation. Here we demonstrate how to use the package with data from the Cancer Genome Atlas.

DOI10.1371/journal.pone.0249002
Alternate JournalPLoS One
PubMed ID33819273
PubMed Central IDPMC8021195
Grant ListP30 CA006973 / CA / NCI NIH HHS / United States
R01 CA200859 / CA / NCI NIH HHS / United States
Related Faculty: 
Luigi Marchionni, M.D., Ph.D.

Pathology & Laboratory Medicine 1300 York Avenue New York, NY 10065 Phone: (212) 746-6464
Surgical Pathology: (212) 746-2700