NormExpr

A matrix of gene expression values where
each row corresponds to a patient and each column is a gene.

expr

A matrix of copy number alterations log2 ratio
where each row corresponds to a patient and each column is a gene.

cna.logr

A character vector of gene HGNC symbols,
default for all genes with both gene expression and
copy number log2 ratio data

gene

A character, either Gaussian process regression  ("gp") or
suppor vector machine regression ("svm")

type

Logical, specifying whether debug information should be printed

debug

Logical, specifying whether to plot the orginal expression
and the normalized expression for a gene

show.plot

Logical, specifying whether to plot the express of
a gene after normalization, only used when <code>show.plot = TRUE</code>.

show.norm


Remove the cis-effects of copy number alterations on gene expression


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.

NormExpr: Remove the cis-effects of copy number alterations on gene expression

Description

Usage

Arguments

Value

Examples