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.