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Methylation Screening Array

QC of cell sorted methylation array data run on the Ilumina Infinium Methylation Screening BeadChip
(https://emea.illumina.com/products/by-type/microarray-kits/infinium-mouse-methylation.html)

This repository contains analysis pipelines for the pre-processing and analysis of the data generated as part of this project. They are developed for use with a HPC system with the SLURM job scheduler.

Guidance for using the pipeline scripts

PREQUISITES:

  • A project folder containing the following sub directories:

    • 0_metadata
    • 1_raw
    • 2_normalised
    • logFiles

  • A config file in the project folder containing file paths and thresholds etc specific to their project

  • A file named sampleSheet.csv in the 0_metadata folder which contains the following columns, and any other associated phenotype data: "Basename","Chip_ID","Chip_Position","Plate", "Individual_ID","Sample_ID","Cell_Type","Study"

  • raw idat files in the 1_raw folder

QUALITY CONTROL STAGE

OUTPUT:

  • Quality control objects, metrics and html reports are located in 2_normalised/QCmetrics

The QCjobSubmission.sh script automates the quality control pipeline and can be run on the command line with: sbatch QCjobSubmission.sh <filepath/to/projectFolder>

This script will execute:

  • calcQCmetrics.r
  • Rscript -e "rmarkdown::render('QC.rmd', output_file='QC.html')" --args $1
  • cellTypeChecks.r
  • Rscript -e "rmarkdown::render('cellTypeQC.rmd', output_file='cellTypeQC.html')"
  • normalisation.r (tba)