methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing

• Main Authors: Kuan, P.F (Author), Ren, X. (Author)
• Format: Article
• Language: English
• Published: Oxford University Press 2018
• Subjects: article; DNA methylation
• Online Access: View Fulltext in Publisher

 Motivation: An important downstream analysis following differential expression from RNA sequencing (RNA-Seq) or DNA methylation analysis is the gene set testing to relate significant genes or CpGs to known biological properties. However, the traditional gene set testing approaches result in biased P-values due to the difference in gene length. Existing methods accounting for length bias were primarily developed for RNA-Seq data. For DNA methylation data profiled using the Illumina arrays, separate methods adjusting for the number of CpGs instead of gene length are necessary. Results: We developed methylGSA, a Bioconductor package for gene set testing in DNA methylation data. Our accompanying Shiny app provides an interactive way of accessing functions and visualizing the results in methylGSA package. © The Author(s) 2018.