dri.merge.CNbyRNA {DRI} | R Documentation |
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.
dri.merge.CNbyRNA(dna.chr, dna.nuc, dna.data, rna.chr, rna.nuc)
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 |
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.
average.dna.data |
a matrix of average DNA copy number values corresponding to each gene expression value |
Keyan Salari, Robert Tibshirani, and Jonathan R. Pollack
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/
drcorrelate
, drcorrelate.null
, drsam
,
drsam.null
, dri.fdrCutoff
, dri.sig_genes
,
dri.heatmap
, dri.merge.CNbyRNA
, dri.smooth.cghdata
,
runFusedLasso
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)