Journal
BIOINFORMATICS
Volume 35, Issue 11, Pages 1958-1959Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/bty892
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Funding
- CDC/NIOSH [U01 OH011478-01]
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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.
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