R: Output gain/loss calls by cghFLasso

output.cghFLasso {cghFLasso} | R Documentation

## Output gain/loss calls by cghFLasso

### 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")

[Package cghFLasso version 0.2-1 Index]