Last data update: 2014.03.03
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R: Remove the cis-effects of copy number alterations on gene...
Remove the cis-effects of copy number alterations on gene expression
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.
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cna.logr |
A matrix of copy number alterations log2 ratio
where each row corresponds to a patient and each column is a gene.
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gene |
A character vector of gene HGNC symbols,
default for all genes with both gene expression and
copy number log2 ratio data
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type |
A character, either Gaussian process regression ("gp") or
suppor vector machine regression ("svm")
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debug |
Logical, specifying whether debug information should be printed
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show.plot |
Logical, specifying whether to plot the orginal expression
and the normalized expression for a gene
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show.norm |
Logical, specifying whether to plot the express of
a gene after normalization, only used when show.plot = TRUE .
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Value
The normalized expression matrix
Examples
data(cna.logr, expr)
expr.norm = NormExpr(cna.logr, expr, gene="PTEN")
Results
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