Get the conditional distributions for a set of genes

Description

Get the conditional distributions for a set of genes

Usage

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GetExpressionDistribution(expr, mut = NULL, cna.call = NULL, gene = NULL,
  type = "student", show.plot = FALSE)

Arguments

expr

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