Limb Enhancer Genie - Source code for model tuning and combining

Model training / parameter tuning

• In your R-session change your working directory to the "model_tuning" folder
• Install the tunetest package

install.packages("./tunetest", repos=NULL, type="source")

• tune_models.R contains the code used to fit chromatin and sequence models
• pre-cumputed output data of this script ('chrom.models.Rdata' & 'seq.models.Rdata') can be found in the "model_combining" folder

Model combining

• In your R-session change your working directory to the "model_combining" folder
• Make sure you have the tunetest package installed (see above)
• combine_models.R contains the code used to combine chromatin and sequence models on the 'leave one out' test sets