GetExpressionDistribution: Get the conditional distributions for a set of genes

In xseq: Assessing Functional Impact on Gene Expression of Mutations in Cancer

Description

Get the conditional distributions for a set of genes

Usage

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

xseq documentation built on May 1, 2019, 9:47 p.m.