SetXseqPrior

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".

A list, the outputs from calling <code>GetExpressionDistribution</code>

expr.dis

Logical, whether considering the directionality
, i.e., up-regulation or down-regulatin of genes, only used
when <code>cis=FALSE</code>.

regulation.direction

Character, only used when <code>cis = TRUE</code>, and can be either
loss, gain or both

mut.type

A hierarchical Bayesian approach to assess functional impact of mutations on gene expression in cancer. Given a patient-gene matrix encoding the presence/absence of a mutation, a patient-gene expression matrix encoding continuous value expression data, and a graph structure encoding whether two genes are known to be functionally related, xseq outputs: a) the probability that a recurrently mutated gene g influences gene expression across the population of patients;
and b) the probability that an individual mutation in gene g in an individual patient m influences expression within that patient.

SetXseqPrior: Set model paramerter priors

Description

Usage

Arguments