Process methylation data using minfi pipeline. This function will drop samples with GT 5 percent high detection p-values, probes with at least one high detection p-value, Sex chromosomes, loci associated with single-nucleotide polymorphisms and cross-hybridizing probes. Additionally, will preprocess using Noob for background correction and dye bias normalization, BMIQ for probe design bias, batch correction using ComBat.

Process methylation data using minfi pipeline. This function will drop samples with GT 5 percent high detection p-values, probes with at least one high detection p-value, Sex chromosomes, loci associated with single-nucleotide polymorphisms and cross-hybridizing probes. Additionally, will preprocess using Noob for background correction and dye bias normalization, BMIQ for probe design bias, batch correction using ComBat.

process_methylation_data(basenames)

Arguments

basenames

list of idat file locations

Value

returns a methyl set