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DMRforPairs (version 1.8.0)

DMRforPairs-package: DMRforPairs package

Description

Please see the DESCRIPTION file.

Arguments

References

  • Bibikova, M., et al.,High density DNA methylation array with single CpG site resolution.Genomics, 2011. 98(4): p. 288-95.
Bibikova, M., et al., Genome-wide DNA methylation profiling using Infinium(R) assay. Epigenomics, 2009. 1(1): p. 177-200. Dedeurwaerder, S., et al., Evaluation of the Infinium Methylation 450K technology. Epigenomics, 2011. 3(6): p. 771-84. Du, P., W.A. Kibbe, and S.M. Lin, lumi: a pipeline for processing Illumina microarray. Bioinformatics, 2008. 24(13): p. 1547-8. Du, P., et al., Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics, 2010. 11: p. 587. Maksimovic, J., L. Gordon, and A. Oshlack, SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome Biol, 2012. 13(6): p. R44. Marabita, F., et al., An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform. Epigenetics, 2013. 8(3): p. 333-46. Pidsley, R., et al., A data-driven approach to preprocessing Illumina 450K methylation array data. BMC Genomics, 2013. 14(1): p. 293. Teschendorff, A.E., et al., A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics, 2013. 29(2): p. 189-96. Touleimat, N. and J. Tost, Complete pipeline for Infinium((R)) Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation. Epigenomics, 2012. 4(3): p. 325-41. Wang, D., et al., IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data. Bioinformatics, 2012. 28(5): p. 729-30. Wilhelm-Benartzi, C.S., et al., Review of processing and analysis methods for DNA methylation array data. Br J Cancer, 2013. 109(6): p. 1394-402. Eckhardt, F., et al., DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet, 2006. 38(12): p. 1378-85. Rijlaarsdam, M.A., et al., DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles. Submitted