R: A function to plot gain/loss calls on CGH arrays

plot.cghFLasso {cghFLasso} | R Documentation

## A function to plot gain/loss calls on CGH arrays

### Description

A function to plot gain/loss calls on CGH arrays

### Usage

    plot.cghFLasso(x, index, type="All", centro=NULL, ...)

### Arguments

`x` | an object of class `cghFLasso` (returned by function `cghFLasso`).
`index` | numeric vector specifying which arrays to plot.
`type` | a character specifying the plot type. It should be one of "Lines", "Single", "Consensus", or "All". See details for more information.
`centro` | numeric vector specifying the centromere positions. If missing, the default centromere value of human genome will be used.
`...` | further arguments passed to or from other methods.

### Details

`plot.cghFLasso` provides several summary plots for `cghFLasso` result object. If `type="Lines"`, it plots the raw CGH measurements and the gain/loss results for the one selected array along the genome (no seperation of chromosomes). If `type="Single"`, it plots the raw CGH measurements and the gain/loss results for the one selected array along the genome (different chromosomes are ploted in different lines). If `type="Consensus"`, it plots the percentages of the gain/loss calls across a group of samples along the genome. If `type="All"`, it plots the results of all selected arrays in one figure.

### Value

It returns the `type` of the plot.

### 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]