cnAnalysis450k: an R package for comparative analysis of 450k/EPIC Illumina methylation array derived copy number data.

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Abstract

Detailed copy number (CN) variation data can be obtained from 450k or EPIC Illumina methylation assays. However, the effects of different preprocessing strategies (normalization, transformation and selection of gain/loss cutoff values) on variant calling have not been evaluated systematically.

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Journal

Journal ID (iso-abbrev): Bioinformatics

Title: Bioinformatics (Oxford, England)

Publisher: Oxford University Press (OUP)

ISSN (Electronic): 1367-4811

ISSN (Print): 1367-4803

Publication date (Electronic): Aug 01 2017

Volume: 33

Issue: 15

Affiliations

[1 ] Department of Radiation Oncology, University Hospital of Heidelberg, Heidelberg 69120, Germany.

[2 ] Clinical Cooperation Unit Radiation Oncology, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.

[3 ] Heidelberg Ion-Beam Therapy Center (HIT), Heidelberg 69120, Germany.

[4 ] Heidelberg Institute for Radiation Oncology (HIRO), University Hospital of Heidelberg, Heidelberg 69120, Germany.

[5 ] Tanslational Radiation Oncology, German Cancer Consortium (DKTK), National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.

Article

Publisher Item ID: 3096425

DOI: 10.1093/bioinformatics/btx156

PubMed ID: 28379302

SO-VID: 68ec7ccb-f1ba-4379-9ca5-3814a487f7b4

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