wateRmelon

"wateRmelon" is a software package designed to enhance the analysis of DNA methylation data, explicitly targeting data generated by the Illumina Infinium HumanMethylation450 (450K) BeadChip. Recognizing DNA methylation as a crucial, stable, and experimentally accessible epigenetic mark, there is a growing need for efficient and cost-effective methods to analyze genome-wide DNA methylation patterns. The 450K BeadChip, while helpful, presents analytical challenges due to its incorporation of two different assay methods, necessitating careful normalization and correction.

To address these challenges, "wateRmelon" utilizes three independent metrics derived from known DNA methylation patterns, including genomic imprinting and X-chromosome inactivation (XCI), as well as the performance of SNP genotyping assays on the array. These metrics serve not only to test various correction and normalization schemes but also as potential quality scores for datasets.