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

Abstract

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. 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. methylGSA is available at Bioconductor repository: https://bioconductor.org/packages/methylGSA and Shiny app is available at: http://www.ams.sunysb.edu/%7epfkuan/softwares.html#methylGSA. Supplementary data are available at Bioinformatics online.