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

Yufang Qin; Hao Feng; Ming Chen; Hao Wu; Xiaoqi Zheng

doi:10.1016/j.gendis.2018.02.003

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

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

Authors

Yufang Qin^{1

2}, Hao Feng³, Ming Chen^{1

2}, Hao Wu³, Xiaoqi Zheng⁴

Affiliations

¹ College of Information Technology, Shanghai Ocean University, Shanghai, 201306, PR China.
² Key Laboratory of Fisheries Information Ministry of Agriculture, Shanghai, 201306, PR China.
³ Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Georgia 30322, USA.
⁴ Department of Mathematics, Shanghai Normal University, Shanghai, 200234, PR China.

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.