R-Programming for Genome-Wide Data Analysis

Abstract

R is a programming language that provides an interface to perform statistical analysis and produce graphics. It is freely available and incorporates precompiled binary functions for various operating systems such as Linux, Mac, and Windows. R is an interactive programming language and contains several pre-defined functions for hypothesis testing in the given dataset. It provides set of operators for handling vector, list, array, or matrices. R helps in coherent, integrated data analysis and also provides facility to incorporate additional libraries containing functions for biological dataset. This chapter provides an overview of various R functions used in genome-wide association studies (GWAS) and elaborated on basic functions with examples as a guideline to GWAS analysis. Additionally, the genome-wide differential expression analysis in cancer dataset along with some of the important packages used in the data processing for quality control, annotation, visualization, and workflow is discussed.