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

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

Description

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

Usage

NormExpr(expr, cna.logr, gene, type = "gp", debug = FALSE,
  show.plot = FALSE, show.norm = TRUE)

Arguments

expr	A matrix of gene expression values where each row corresponds to a patient and each column is a gene.
cna.logr	A matrix of copy number alterations log2 ratio where each row corresponds to a patient and each column is a gene.
gene	A character vector of gene HGNC symbols, default for all genes with both gene expression and copy number log2 ratio data
type	A character, either Gaussian process regression ("gp") or suppor vector machine regression ("svm")
debug	Logical, specifying whether debug information should be printed
show.plot	Logical, specifying whether to plot the orginal expression and the normalized expression for a gene
show.norm	Logical, specifying whether to plot the express of a gene after normalization, only used when show.plot = TRUE.

Value

The normalized expression matrix

Examples

data(cna.logr, expr)
expr.norm = NormExpr(cna.logr, expr, gene="PTEN")

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