A data.frame of mutations. The data.frame should have
three columns of characters: sample, hgnc_symbol, and variant_type.
The variant_type column cat be either "HOMD", "HLAMP",
"MISSENSE", "NONSENSE", "FRAMESHIFT", "INFRAME", "SPLICE", "NONSTOP",
"STARTGAINED", "SYNONYMOUS", "OTHER", "FUSION", "COMPLEX".
expr
A matrix of gene expression values where
each row corresponds to a patient and each column is a gene
net
A list of gene interaction networks
expr.dis
The fitted gene expression distributions,
output from GetExpressionDistribution
prior
The prior for xseq, output from SetXseqPrior
cpd
A list of conditional probability tables for xseq,
output from SetXseqPrior
gene
A character vector of gene names,
default to all the genes with mutations
p.h
The down-regulation probability list of each gene
connected to a mutated gene,
typically from running LearnXseqParameter
on a discovery dataset
weight
The weight list of each gene
connected to a mutated gene,
typically from running LearnXseqParameter
on a discovery dataset
providing 
.