CREATION OF DIFFERENTIALLY METHYLATED BACKGROUND GENE SET FOR GO ENRICHMENT

<br>SUMMARYThis script prepares a background gene set for GO enrichment analysis based on differentially methylated CpGs in <i>Nasonia vitripennis</i> 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.<br><br>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 set<br>INPUT FILES<br>- 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 genes<br>OUTPUT FILES<br>- diff_methylatedcpgs_with_LOC.csv: CpGs mapped to annotated gene features- diff_backgroundGOannotations.csv: Final gene-GO background used for enrichment<br>SOFTWARE REQUIREMENTS<br>- R packages: data.table, dplyr, tidyr, readr, sqldf, GOstats, GSEABase, treemap- Input genome annotation must contain numbered exon/intron coordinates and gene_id mappings<br>NOTES- 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)<br><br><br>CONTACT<br>Eamonn Mallon [e-mail]<br>