Torch-eCpG: a fast and scalable eQTM mapper for thousands of molecular phenotypes with GPUs

Gene expression may be regulated by the DNA methylation of regulatory elements in promoter, gene-body, cis, distal, and trans regions. One method to evaluate the relationship between DNA methylation and gene expression is the mapping of expression quantitative trait methylation (eQTM) loci (also called expression-associated CpG loci, eCpG). However, no open-source tools are available to provide eQTM mapping. In addition, eQTM mapping can involve a large number of comparisons which may prevent the analyses due to limitations of computational resources. Here, we describe Torch-eCpG (tecpg), an open-source tool developed in Python to perform eQTM mapping that includes an optimized implementation that can use the graphical processing unit (GPU) to reduce runtime.