Format

Send to

Choose Destination
F1000Res. 2018 Dec 5;7. pii: ISCB Comm J-1897. doi: 10.12688/f1000research.16338.1. eCollection 2018.

An accessible GenePattern notebook for the copy number variation analysis of Illumina Infinium DNA methylation arrays.

Author information

1
Department of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
2
Moores Cancer Center, University of California, San Diego, La Jolla, CA, 92093, USA.

Abstract

Illumina Infinium DNA methylation arrays are a cost-effective technology to measure DNA methylation at CpG sites genome-wide and across cohorts of normal and cancer samples. While copy number alterations are commonly inferred from array-CGH, SNP arrays, or whole-genome DNA sequencing, Illumina Infinium DNA methylation arrays have been shown to detect copy number alterations at comparable sensitivity. Here we present an accessible, interactive GenePattern notebook for the analysis of copy number variation using Illumina Infinium DNA methylation arrays. The notebook provides a graphical user interface to a workflow using the R/Bioconductor packages minfi and conumee. The environment allows analysis to be performed without the installation of the R software environment, the packages and dependencies, and without the need to write or manipulate code.

KEYWORDS:

DNA methylation; GenePattern Notebook; Illumina Infinium methylation arrays; Jupyter Notebook; R/Bioconductor; conumee; copy number variation; interactive; minfi; open-source; pre-processing; visualization

Supplemental Content

Full text links

Icon for F1000 Research Ltd Icon for PubMed Central
Loading ...
Support Center