dri.heatmap {DRI} | R Documentation |
A heatmap is generated showing the DNA copy number and gene expression data for the significant, positively correlated DR-Correlate genes.
dri.heatmap(Results.SigGenes, DNA, RNA, SampleIDs, GeneNames, Chr, Nuc, statistic, color.scheme)
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) |
Keyan Salari, Robert Tibshirani, 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) # 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()