drsam.null {DRI}R Documentation

Generate null distribution for DR-SAM analysis

Description

A null distribution is generated by randomly permuting the class labels of the samples and recomputing the DR-SAM statistic for each gene.

Usage

drsam.null(DNA.data, RNA.data, labels, transform.type, k)

Arguments

DNA.data matrix of DNA copy number data
RNA.data matrix of gene expression data, samples (columns) in same order as DNA matrix
labels class labels of the two comparison groups, either 1 or 2
transform.type type of transformation to apply to data, either "standardize", "rank", or "raw"
k 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, 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-SAM analysis to find genes with alterations in both DNA and RNA between
# different classes
labels <- c(rep(1,25), rep(2,25)) # 25 samples in class 1 and 25 in class 2
obs <- drsam(DNA.data, RNA.data, labels, transform.type="raw")
# generate null distribution for FDR calculation (10 permutations)
null <- drsam.null(DNA.data, RNA.data, labels, transform.type="raw", 10)
# identify the correlation cutoff corresponding to your desired FDR
n.cutoff <- dri.fdrCutoff(obs$test.summed, 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="drsam") 

[Package DRI version 1.1 Index]