A matrix of gene expression values where
each row corresponds to a patient and each column is a gene.
mut
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".
cna.call
A matrix containing the copy number calls, where each element is coded:
-2, homozygous deletions
-1, hemizygous deletions
0, neutral
1, gain
2, amplifications
gene
A character vector of official HGNC gene names
type
Character, either Gaussian ("gauss") or
Student ("student")
show.plot
Logical, specifying whether to plot the fitted model
Value
A list containg the fitted expression distributions