runFusedLasso {DRI} | R Documentation |
A function to run the Fused Lasso method on DNA copy number data to call copy number alterations.
runFusedLasso(DNA.data, normal.data = NA, chr, nuc, FDR)
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 |
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.
data.FL |
matrix of DNA copy number data with significant gains and losses called by Fused Lasso, and non-significant changes set to zero |
Keyan Salari, Robert Tibshirani, and 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/
Tibshirani, R., and Wang, P. (2008) Spatial smoothing and hot spot detection for CGH data using the fused lasso, Biostatistics, 9, 18-29.
drcorrelate
, drcorrelate.null
, drsam
,
drsam.null
, dri.fdrCutoff
, dri.sig_genes
,
dri.heatmap
, dri.merge.CNbyRNA
, dri.smooth.cghdata
,
runFusedLasso
library(cghFLasso) data(CGH) attach(CGH) DRI.DNA.data.FL <- runFusedLasso(DNA.data=DiseaseArray, normal.data=NormalArray, chr=chromosome, nuc=nucposition, FDR=0.01)