CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array.

ABSTRACT:

Unlabelled

The Illumina Infinium HumanMethylation450 BeadChip (450k) is widely used for the evaluation of DNA methylation levels in large-scale datasets, particularly in cancer. The 450k design allows copy number variant (CNV) calling using existing bioinformatics tools. However, in cancer samples, numerous large-scale aberrations cause shifting in the probe intensities and thereby may result in erroneous CNV calling. Therefore, a baseline correction process is needed. We suggest the maximum peak of probe segment density to correct the shift in the intensities in cancer samples.

Availability and implementation

CopyNumber450kCancer is implemented as an R package. The package with examples can be downloaded at http://cran.r-project.org

Contact

[e-mail]

SUBMITTER: Marzouka NA 

PROVIDER: S-EPMC4896365 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature