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: nour.marzouka@medsci.uu.se
Supplementary Information: Supplementary data are available at Bioinformatics online.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896365 | PMC |
| http://dx.doi.org/10.1093/bioinformatics/btv652 | DOI Listing |
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