inst/scripts/synthetic_benchmark/README.md

In kpj/dce: Pathway Enrichment Based on Differential Causal Effects

Benchmarking

Benchmark dce method on synthetic data with the goal of understanding how our algorithm behaves under a wide range of parameters.

Automated

All important benchmarks shall be defined in config/config.yaml. They can then be executing as follows:

$ snakemake -pr -j 1

Manual

Specific configurations can be easily tested:

$ Rscript workflow/scripts/main.R --variable node.num --values "25,50,100,200" --methods "dce,dce.lm" --replicates 10
$ Rscript workflow/scripts/plotting.R

kpj/dce documentation built on Oct. 29, 2022, 1:40 a.m.