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.
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
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)