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Open Access

InfiniumPurify: An R package for estimating and accounting for tumor purity in cancer methylation research

Yufang Qina,b, Hao Fengc, Ming Chena,b, Hao Wuc, Xiaoqi Zhengd,( )
College of Information Technology, Shanghai Ocean University, Shanghai, 201306, PR China
Key Laboratory of Fisheries Information Ministry of Agriculture, Shanghai, 201306, PR China
Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Georgia 30322, USA
Department of Mathematics, Shanghai Normal University, Shanghai, 200234, PR China

Peer review under responsibility of Chongqing Medical University.

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Abstract

The proposition of cancer cells in a tumor sample, named as tumor purity, is an intrinsic factor of tumor samples and has potentially great influence in variety of analyses including differential methylation, subclonal deconvolution and subtype clustering. InfiniumPurify is an integrated R package for estimating and accounting for tumor purity based on DNA methylation Infinium 450 k array data. InfiniumPurify has three main functions getPurity, InfiniumDMC and InfiniumClust, which could infer tumor purity, differential methylation analysis and tumor sample cluster accounting for estimated or user-provided tumor purities, respectively. The InfiniumPurify package provides a comprehensive analysis of tumor purity in cancer methylation research.

Keywords

DNA methylationCancer subtype classificationDifferential methylation analysisTumor purityInfiniumPurify

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Genes & Diseases
Volume 5 Issue 1,
March 2018
Pages 43-45
DOI: 10.1016/j.gendis.2018.02.003
Cite this article:
Qin Y, Feng H, Chen M, et al. InfiniumPurify: An R package for estimating and accounting for tumor purity in cancer methylation research. Genes & Diseases, 2018, 5(1): 43-45. https://doi.org/10.1016/j.gendis.2018.02.003

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Received: 02 February 2018
Accepted: 04 February 2018
Published: 21 February 2018
© 2018, Chongqing Medical University.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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