dri.heatmap {DRI}R Documentation

Generate a heatmap of significant DR-Correlate genes

Description

A heatmap is generated showing the DNA copy number and gene expression data for the significant, positively correlated DR-Correlate genes.

Usage

dri.heatmap(Results.SigGenes, DNA, RNA, SampleIDs, GeneNames, Chr, 
Nuc, statistic, color.scheme)

Arguments

Results.SigGenes list of significant genes from dri.sig_genes
DNA matrix of DNA copy number data
RNA matrix of gene expression data, samples (columns) in same order as DNA matrix
SampleIDs vector of sample names
GeneNames vector of gene names
Chr vector of gene chromosome locations
Nuc vector of gene nucleotide positions
statistic method used in drcorrelate, either "pearson", "spearman", or "ttest"
color.scheme desired heatmap color scheme, either "RG" (red-green), "RB" ("red-blue), or "YB" (yellow-blue)

Author(s)

Keyan Salari, Robert Tibshirani, 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)

# DNA data should contain no missing values - pre-smooth beforehand
# Impute missing values for gene expression data
RNA.data <- dri.impute(RNA.data)

# DR-Correlate analysis to find genes with correlated DNA/RNA measurements
obs <- drcorrelate(DNA.data, RNA.data, method="pearson")
# generate null distribution for FDR calculation (10 permutations)
null <- drcorrelate.null(DNA.data, RNA.data, method="pearson", perm=10)
# identify the correlation cutoff corresponding to your desired FDR
n.cutoff <- dri.fdrCutoff(obs, null, targetFDR=0.05, bt=TRUE)
cutoff <- n.cutoff[2]
# retrieve all genes that are significant at the determined cutoff, and
# calculate gene-specific FDRs
Results <- dri.sig_genes(cutoff, obs, null, GeneIDs, GeneNames, Chr, Nuc, 
bt=TRUE, method="drcorrelate") 

# Optional heatmap plot for significant DR-Correlation genes
sample.names <- colnames(DNA.data)
pdf(file="DRI-Heatmap.pdf", height=8, width=11)
dri.heatmap(Results, DNA.data, RNA.data, sample.names, GeneNames, Chr, Nuc, 
statistic="pearson", color.scheme="RG")
dev.off()

[Package DRI version 1.1 Index]