Package: cpgdirection 2.99.5

cpgdirection: Predict the Direction of CpG-Gene Expression Associations

Assigns a direction to the association between DNA methylation at a CpG site and the expression of a nearby gene, for CpGs that have no measured expression quantitative trait methylation (eQTM) record. Predictions come from a precomputed table of 3,105,697 CpG-gene pairs covering 761,445 CpGs, assembled from four sources of evidence: directly measured eQTMs, summary-data Mendelian randomisation using genetic instruments, gradient-boosted models of genomic context and local catalogue structure fitted separately in blood, nasal epithelium and solid tissue, and a distance prior. Each call returns a direction, a calibrated probability, an evidence tier and an expected accuracy, and abstains where the evidence is insufficient. Predictions estimate direction conditional on the CpG being an eQTM; they do not establish that an effect exists.

Authors:Tsachi Ein-Dor [aut, cre, fnd]