dri.correlation.plot {DRI}R Documentation

Plot significant correlations from DR-Correlate analysis

Description

A plot is generated of all the correlations computed by DR-Correlate, indicating significant correlations in red (positive) or blue (negative), ordered by chromosomal coordinates.

Usage

dri.correlation.plot(observed, Results.SigGenes, sig_cutoff, chr, 
nuc_pos, bothtails)

Arguments

observed vector of observed correlations from drcorrelate
Results.SigGenes list of significant genes from dri.sig_genes
sig_cutoff correlation significance cutoff returned from dri.fdrCutoff
chr vector of gene chromosome locations
nuc_pos vector of gene nucleotide positions
bothtails TRUE or FALSE indicating whether 2-tail test was performed

Value

plot a plot of the correlations is returned in chromosomal order, with significant correlations marked in red (positive) and blue (negative)

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 correlation plot for significant DR-Correlation genes
dri.correlation.plot(obs, Results, cutoff, Chr, Nuc, bothtails=TRUE)

[Package DRI version 1.1 Index]