Codes used for the analysis of blood methylation levels in Filipino patients with Type 2 Diabetes. Maintained by Dominic S. Albao.
Contains MD5 checksums of the raw Illumina intensitiy files (IDAT) in order to check for corruption during data transfers.
Contains the updated manifest file for the Illumina MethylationEPIC beadchip mapped to human reference genome GRCh38. The manifest is supplied as a larged TSV file (ignored by Git) with special annotations by Zhou and others (2017, doi:10.1093/nar/gkw967) on recommended masking settings for probes with SNPs and high copy numbers.
Contains output from analyses on the methylation data.
Contains scripts written in PERL used for the manipulation of data prior to import and analysis using R.
Contains scripts for the analysis of methylation data from raw Illumina intensity files (IDAT) using R.
Contains the raw Illumina intensity files (IDAT). Git is set to ignore IDAT files in order to avoid hitting storage quotas on Git. If you need a copy of the raw data, (currently a total of 6.1 GB), contact me. This folder also contains Sample Sheets describing the location, identity and characterisitcs of each sample.
Contains bash scripts for the manipulation of files and datasets prior to analysis in R. Also contains scripts for pipelining separate PERL, R and bash scripts cohesively.