I'm trying to run quality control on the new Illumina EPIC chip methylation data with the meffil packages. I've used it with the Illumina 450k previously and then I've used the following command:
qc.parameters <- meffil.qc.parameters(beadnum.samples.threshold = 0.1, detectionp.samples.threshold = 0.1, detectionp.cpgs.threshold = 0.1, beadnum.cpgs.threshold = 0.1, sex.outlier.sd = 5, snp.concordance.threshold = 0.95, sample.genotype.concordance.threshold = 0.8)
qc.summary <- meffil.qc.summary(qc.objects, parameters = qc.parameters, genotypes=genotypes)
But for the 450K I've then had a genotype file. For the EPIC chip I just have the .idat files. Does anyone know how to call the genotypes from the EPIC chip?