runFusedLasso {DRI}R Documentation

Wrapper function to run cghFLasso

Description

A function to run the Fused Lasso method on DNA copy number data to call copy number alterations.

Usage

runFusedLasso(DNA.data, normal.data = NA, chr, nuc, FDR)

Arguments

DNA.data matrix of disease tissue DNA copy number data
normal.data matrix of normal tissue DNA copy number data (optional)
chr vector of chromosomes where copy number probes are located (ordered by genome location)
nuc numeric vector of nucleotide positions where copy number probes are located (ordered by genome location)
FDR false discovery rate to apply to threshold significant gains and losses

Details

This function performs a pre-processing step to smooth and segment DNA copy number data using the fused lasso method of Tibshirani & Wang, 2008. The DNA copy number data from the disease tissues are compared to that of normal tissues, if supplied, to help call significant copy number alterations. A false discovery rate is calculated for each copy number alteration and the significance threshold is user-definable. More details of the Fused Lasso method can be found with the cghFLasso package and in the reference below.

Value

data.FL matrix of DNA copy number data with significant gains and losses called by Fused Lasso, and non-significant changes set to zero

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/

Tibshirani, R., and Wang, P. (2008) Spatial smoothing and hot spot detection for CGH data using the fused lasso, Biostatistics, 9, 18-29.

See Also

drcorrelate, drcorrelate.null, drsam, drsam.null, dri.fdrCutoff, dri.sig_genes, dri.heatmap, dri.merge.CNbyRNA, dri.smooth.cghdata, runFusedLasso

Examples

library(cghFLasso)
data(CGH)
attach(CGH)

DRI.DNA.data.FL <- runFusedLasso(DNA.data=DiseaseArray, 
normal.data=NormalArray, chr=chromosome, nuc=nucposition, FDR=0.01)

[Package DRI version 1.1 Index]