dri.merge.CNbyRNA {DRI}R Documentation

Merge DNA copy number and gene expression data sets

Description

A matrix of DNA copy number values and a matrix of gene expression values are merged into one matrix using the genome position coordinates of the probes on each microarray platform. Copy number probes flanking each gene expression probe are averaged to derive the copy number at a given expression probe.

Usage

dri.merge.CNbyRNA(dna.chr, dna.nuc, dna.data, rna.chr, rna.nuc)

Arguments

dna.chr vector of chromosomes on which copy number probes are located
dna.nuc numeric vector of nucleotide positions where copy number probes are located
dna.data matrix of DNA copy number data
rna.chr vector of chromosomes on which expression probes are located
rna.nuc numeric vector of nucleotide positions where expression probes are located

Details

This function performs a pre-processing step to obtain 1-to-1 mappings of DNA copy number and gene expression for each measured gene. For each gene expression probe, the closest 5' and 3' copy number probes are used to calculate an average copy number value. If the same array platform was used to measure copy number and gene expression, the copy number and gene expression measurement will be matched by the probes' genome position coordinates. This function returns a DNA copy number matrix that has the same number of rows (genes) as the gene expression matrix.

Value

average.dna.data a matrix of average DNA copy number values corresponding to each gene expression value

Author(s)

Keyan Salari, Robert Tibshirani, and Jonathan R. Pollack

References

Salari, K., Tibshirani, R., and Pollack, J.R. (2009) DR-Integrator: a new analytic tool for integrating DNA copy number and gene expression data. http://pollacklab.stanford.edu/

See Also

drcorrelate, drcorrelate.null, drsam, drsam.null, dri.fdrCutoff, dri.sig_genes, dri.heatmap, dri.merge.CNbyRNA, dri.smooth.cghdata, runFusedLasso

Examples

require(impute)
data(mySampleData)
attach(mySampleData)

dri.merge.CNbyRNA(dna.chr=Chr, dna.nuc=Nuc, dna.data=DNA.data, rna.chr=Chr, 
rna.nuc=Nuc)

[Package DRI version 1.1 Index]