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. 2018 Feb 21;5(1):43-45.
doi: 10.1016/j.gendis.2018.02.003. eCollection 2018 Mar.

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

Yufang Qin  1   2 , Hao Feng  3 , Ming Chen  1   2 , Hao Wu  3 , Xiaoqi Zheng  4
Affiliations

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

Yufang Qin et al. Genes Dis. .

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: Cancer subtype classification; DNA methylation; Differential methylation analysis; InfiniumPurify; Tumor purity.

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Figures

Figure 1
Figure 1
An example showing DMCs that are only detected by InfiniumPurify. Left panel shows their methylation level distributions in tumor and normal samples. Middle panel shows correlation between purities and methylation levels. Right panel shows methylation levels of normal and tumor samples after correcting for tumor purities.
See this image and copyright information in PMC

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