Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2012 May 1;28(9):1280-1.
doi: 10.1093/bioinformatics/bts124. Epub 2012 Mar 25.

CpGassoc: an R function for analysis of DNA methylation microarray data

Richard T Barfield  1 , Varun Kilaru, Alicia K Smith, Karen N Conneely
Affiliations

CpGassoc: an R function for analysis of DNA methylation microarray data

Richard T Barfield et al. Bioinformatics. .

Abstract

Summary: With the increasing availability of high-density methylation microarrays, there has been growing interest in analysis of DNA methylation data. We have developed CpGassoc, an R package that can efficiently perform the statistical analysis needed for increasingly large methylation datasets. CpGassoc is a modular, expandable package with functions to perform rapid analyses of DNA methylation data via fixed or mixed effects models, to perform basic quality control, to carry out permutation tests, and to display results via an array of publication-quality plots.

Availability and implementation: CpGassoc is implemented in R and is freely available at http://genetics.emory.edu/conneely; we are in the process of submitting it to CRAN.

PubMed Disclaimer

Figures

Fig. 1.
Fig. 1.
Plots from CpGassoc: (A) Q–Q plot, (B) scatterplot, (C) boxplot and (D) Manhattan plot.
See this image and copyright information in PMC

References

    1. Bell J.T., et al. DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 2011;12:R10. - PMC - PubMed
    1. Benjamini Y. The control of the false discovery rate in multiple testing under dependency. Ann. Stat. 2001;4:1165–1188.
    1. Bibikova M., et al. High density DNA methylation array with single CpG site resolution. Genomics. 2011;98:288–295. - PubMed
    1. Breitling L.P., et al. Tobacco-smoking-related differential DNA methylation: 27K discovery and replication. Am. J. Hum. Genet. 2011;88:450–457. - PMC - PubMed
    1. Dabney A., et al. qvalue: Q-value Estimation for False Discovery Rate Control. Vienna: R Foundation for Statistical Computing; 2012. R package version 1.28.0.