output.cghFLasso: Output gain/loss calls by cghFLasso

In cghFLasso: Detecting hot spot on CGH array data with fused lasso regression.

Description

Output gain/loss calls by cghFLasso.

Usage

    output.cghFLasso(summary.obj, file, gene.info=NULL)  

Arguments

summary.obj	an object of class summary.cghFLasso, usually, a result of a call to summary.cghFLasso.
file	a character specifying the file name to output the data.
gene.info	matrix. Additional gene/clone annotation to output.

Details

Output gain/loss calls by cghFLasso.

Value

No return value.

Author(s)

N. A. Johnson, R. Tibshirani and P. Wang

References

R. Tibshirani, M. Saunders, S. Rosset, J. Zhu and K. Knight (2004) ‘Sparsity and smoothness via the fused lasso’, J. Royal. Statist. Soc. B. (In press), available at http://www-stat.stanford.edu/~tibs/research.html.

P. Wang, Y. Kim, J. Pollack, B. Narasimhan and R. Tibshirani (2005) ‘A method for calling gains and losses in array CGH data’, Biostatistics 2005, 6: 45-58, available at http://www-stat.stanford.edu/~wp57/CGH-Miner/

R. Tibshirani and P. Wang (2007) ‘Spatial smoothing and hot spot detection using the Fused Lasso’, Biostatistics (In press), available at http://www-stat.stanford.edu/~tibs/research.html.

J. Friedman, T. Hastie. R. Tibshirani (2007) ‘Pathwise coordinate optimization and the fused lasso’.

Examples

library(cghFLasso)
data(CGH)

#############
### Example 1: Process one chromosome vector without using normal references.

CGH.FL.obj1<-cghFLasso(CGH$GBM.y)
plot(CGH.FL.obj1, index=1, type="Lines")

#############
### Example 2: Process a group of CGH arrays and use normal reference arrays.

Normal.FL<-cghFLasso.ref(CGH$NormalArray,  chromosome=CGH$chromosome)
Disease.FL<-cghFLasso(CGH$DiseaseArray, chromosome=CGH$chromosome, nucleotide.position=CGH$nucposition, FL.norm=Normal.FL, FDR=0.01)

###  Plot for the first arrays
i<-1
plot(Disease.FL, index=i, type="Single")
title(main=paste("Plot for the ", i ,"th BAC array", sep=""))

### Consensus plot
plot(Disease.FL, index=1:4, type="Consensus")
title(main="Consensus Plot for 4 BAC arrays")

### Plot all arrays
plot(Disease.FL, index=1:4, type="All")
title(main="Plot for all 4 arrays")

### Report and output
report<-summary(Disease.FL, index=1:4)
print(report)
output.cghFLasso(report, file="CGH.FL.output.txt")

cghFLasso documentation built on May 29, 2017, 7:18 p.m.