This is a collection of R scripts that handle methylation data from Illumina arrays. They perform pre-processing of the data, quality checks, confounder check, and find DMPs (differentially methylated positions) and DMRs (differentially methylated regions).
Order of the scripts: pre_processing_1.R
##The following 2 scripts can come in any order xreactive_probes_find_remove_2.R remove_snp_probes_3.R
##The following scripts are optional and can be used in any order remove_sex_chromosomes_o1.R remove_confounding_probes_o2.R adjust_cell_composition_o3.R adjust_batch_effect_o4.R
##The following 2 scripts are mandatory and should be run in the following order find_dmp_4.R find_dmr_5.R
##The following script can be optional find_blocks_6.R