methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing
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...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
Oxford University Press
2018
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| Subjects: | |
| Online Access: | View Fulltext in Publisher |
| Summary: | 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. |
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| ISBN: | 13674803 (ISSN) |
| DOI: | 10.1093/BIOINFORMATICS/BTY203 |