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Table 2 R packages and instructions. Specific instructions used from each R package

From: DNA methylation levels are highly correlated between pooled samples and averaged values when analysed using the Infinium HumanMethylation450 BeadChip array

R package Instruction Description
methylumi methylumiR Load Illumina methylation data into a MethyLumiSet object.
minfi densityPlot Density plots of methylation Beta values.
watRmelon pfilter Filter data sets based on bead count and detection p-values
minfi mdsPlot Multi-dimensional scaling (MDS) plots showing a 2-d projection of distances between samples.
watRmelon dasen Calculate normalized betas from Illumina 450 K methylation arrays.
lumi estimateBetas Estimate methylation Beta-value matrix from eSet-class object (include methylated and unmethylated probe intensities)