drcorrelate.null {DRI}R Documentation

Generate null distribution for DR-Correlate analysis

Description

A null distribution is generated by randomly permuting the sample labels of the gene expression data matrix and recomputing the DNA/RNA correlations for each gene.

Usage

drcorrelate.null(DNA, RNA, method = "pearson", tail_p = 10, perm)

Arguments

DNA matrix of DNA copy number data
RNA matrix of gene expression data, samples (columns) in same order as DNA matrix
method correlation statistic, either "pearson", "spearman", or "ttest"
tail_p top/bottom percent of samples (with respect to the gene's copy number) to use for extremes t-test groups; used only when method = "ttest"
perm number of permutations to perform

Value

null n * k matrix of null data, where n = number of genes and k = number of permutations

Author(s)

Keyan Salari, Robert Tibshirani, and 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") 

[Package DRI version 1.1 Index]