CopyNumber450kCancer
Computational Tool
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General Information
DescriptionBaseline correction for accurate copy number calling from the 450k methylation array
Homepagehttp://cran.r-project.org
Publications
CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array
Nour-al-dain Marzouka; Jessica Nordlund; Christofer L. Bäcklin; Gudmar Lönnerholm; Ann-Christine Syvänen; Jonas Carlsson Almlöf
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: nour.marzouka@medsci.uu.se
Supplementary information: Supplementary data are available at Bioinformatics online.
DOI: https://doi.org/10.1093/bioinformatics/btv652
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