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Table 3 Benchmarking time consumption of GEM implementations on Emodel, Gmodel and GxEmodel by comparing normal R script in a public available dataset in standard laptop and HPC settings

From: Gene, Environment and Methylation (GEM): a tool suite to efficiently navigate large scale epigenome wide association studies and integrate genotype and interaction between genotype and environment

  Dataset: Teh et al., 1423 CpGs, 708,365 SNPs and 19 environments in a standard laptop
Method Time cost on standard laptop Time cost in HPC Method Time cost
LM_Emodel 95.1 s   GEM_Emodel 18.9 s
LM_Gmodel > = 60 days (a) 3 h GEM_Gmodel 5.2 min
LM_GxEmodel > = 60 days (a) 21 h GEM_GxEmodel 1.5 h
  1. aThe time for LM_Gmodel and LM_GxEmodel in standard laptop was computed based on the time cost on 10 CpGs