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Fig. 2 | Epigenetics & Chromatin

Fig. 2

From: MethylToSNP: identifying SNPs in Illumina DNA methylation array data

Fig. 2

a MethylToSNP can be integrated in existing methylation array processing pipelines, where the source data can originate from remote data sources, such as GEO or local files. MethylToSNP requires already preprocessed data and will merge the SNP predictions with existing SNP annotations if available. This is why we recommend using it in conjunction with Bioconductor minfi package. b Schematic representation of the MethylToSNP workflow. Given a minfi object or a plain matrix, MethylToSNP will extract beta-values and will process one ‘cg’ probe at a time. For each probe, methylation values in different samples are clustered to find gaps between clusters with optional outlier exclusion (see “Methods”). The gaps are tested against the thresholds passed as the program’s parameters. Predicted SNPs are then reported along with the existing SNP annotation when available. Reliability scores are calculated to emphasize detection of patterns consistent with meC > T transitions

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