dri.correlation.plot {DRI} | R Documentation |
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.
dri.correlation.plot(observed, Results.SigGenes, sig_cutoff, chr, nuc_pos, bothtails)
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 |
plot |
a plot of the correlations is returned in chromosomal order, with significant correlations marked in red (positive) and blue (negative) |
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 correlation plot for significant DR-Correlation genes dri.correlation.plot(obs, Results, cutoff, Chr, Nuc, bothtails=TRUE)