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