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methylation_array_processing

These scripts perform DNA methylation array pre-processing - filtering & normalization Follows the first steps outlined in Wilhelm-Benartzi et al. 2013 (see Figure 1 and Table 1)

I recommend creating a new environment (i.e. using conda) to install all required software. First install R version 3.5.1 (this older version avoids package conflicts), then install the following:

CRAN R packages: RPMM

Bioconductor R packages: minfi wateRmelon IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICanno.ilm10b4.hg19 FlowSorted.Blood.450k FlowSorted.Blood.EPIC

-- RUNNING THE PIPELINE --

  1. Copy all scripts to a working directory
  2. Specify all desired options for the R scripts within 'process_methylation_data.sh', including adding paths to .idats, sample sheets, etc.
  3. Set up and activate the working environment as described above
  4. Execute 'process_methylation_data.sh'