Step 3. Advanced running

Fix ridge penalty value λ

If there is a known value of ridge penalty or is required to fine-grained tuning of the result, a fixed penalty value λ can be used.

  • (--prolambda) Pre-determined lambda(λ) value. --cv option will not required if use this option.

The following example demonstrates usage of fixed penalty value λ.

# For Linux distributions
pharaoh@JOB1:~/foo$ ./pharaoh --pharaoh --prolambda 155 --ped dataset.ped --set gene.set --geneset pathway.set

# For Microsoft Windows
C:\foo> pharaoh --pharaoh --prolambda 155 --ped dataset.ped --set gene.set --geneset pathway.set

--pharaoh command let the PHARAOH program performs PHARAOH analysis.

--prolambda fixes the λ parameter.

--ped, --set and --geneset indicate the dataset, variants-gene mapping and genes-pathway mapping, respectively.