CREATION OF DIFFERENTIALLY METHYLATED BACKGROUND GENE SET FOR GO ENRICHMENT

SUMMARYThis script prepares a background gene set for GO enrichment analysis based on differentially methylated CpGs in Nasonia vitripennis from an ageing (diapause) methylation dataset. It filters CpGs, maps them to genomic features, and annotates them with gene identifiers (gene_id) using exon/intron reference data. GO annotations are then assigned to generate a background for downstream enrichment testing.KEY STEPS1. Load Erin's methylation data (erindata_v2.txt)2. Filter for CpGs in the ageing-related DML list (timepoint DMLs)3. Extract chromosome and position from CpG row identifiers4. Join CpG positions with exon/intron gene annotations (Nvit genome)5. Retain only those CpGs overlapping gene features6. Assign GO terms to mapped gene_ids using Nasonia GO file7. Output the resulting gene-GO annotation file as a background setINPUT FILES- erindata_v2.txt: Erin's filtered methylation matrix- un.dmls.timepoint.txt: Differentially methylated CpG list (timepoint only)- GCF_009193385.2_Nvit_psr_1.1_genomic_numbered_exons.txt: Nasonia exon/intron annotation- Nasonia_PSR1.1_Gene_GO.txt: GO annotations for Nasonia genesOUTPUT FILES- diff_methylatedcpgs_with_LOC.csv: CpGs mapped to annotated gene features- diff_backgroundGOannotations.csv: Final gene-GO background used for enrichmentSOFTWARE REQUIREMENTS- R packages: data.table, dplyr, tidyr, readr, sqldf, GOstats, GSEABase, treemap- Input genome annotation must contain numbered exon/intron coordinates and gene_id mappingsNOTES- GO evidence code is set to "IEA" for all terms- CpGs not overlapping gene features are excluded from the background- This background set is later used in GO enrichment scripts (see Table S4 analysis)CONTACTEamonn Mallon [e-mail]