clac.PlotAllArray.R {clac}R Documentation

A function to plot multiple arrays for CLAC result.

Description

A function to plot multiple arrays for CLAC result.

Usage

clac.PlotAllArray.R(NormalResult, clac.result, ArrayName=NULL,centromere=NULL)

Arguments

NormalResult result object of function clac.preparenormal.R
clac.result result object of function clac.tumorarray.R
ArrayName string vector, providing the name of each disease array in clac.result. The length should be the same as the total number of disease arrays.
centromere numeric vector specifying the centromere positions. If missing, the default centromere value of human genome will be used.

Details

clac.PlotAllArray.R plot multiple array for CLAC result.

Value

No return value.

Author(s)

Pei Wang

References

P. Wang, Y. Kim, J. Pollack, B. Narasimhan and R. Tibshirani, ¡°A method for calling gains and losses in array CGH data¡±, Biostatistics (accepted for publication 4/5/2004), available at http://www-stat.stanford.edu/~wp57/CGH-Miner/

Examples

library(clac)
data(BACarray)
attach(BACarray)

############ prepare the normal reference arrays
NormalResult<-clac.preparenormal.R(DiseaseArray, NormalArray, Normal.Type=rep(0,3), chromosome.number=chromosome, nucleotide.position=nucposition, windowsize=5, targetFDR=0.01, chromosomeOption=FALSE)

############ clac on selected tumor arrays
clac.result<-clac.tumorarray.R(NormalResult, tumorarrayIndex=1:4)

############ Plot for the first arrays
i<-1
clac.PlotSingleArray.R(i, NormalResult, clac.result)
title(main=paste("CLAC Plot for the ", i ,"th BAC array; FDR=", round(clac.result$fdr[i],3), sep=""))

############ consensus plot
clac.PlotConsensus.R(clac.result, chromosome, nucposition,  1:4)
title(main="Consensus Plot for 4 BAC arrays")

############ Plot all arrays
clac.PlotAllArray.R(NormalResult, clac.result)
title(main="Plot for all 4 arrays")

[Package clac version 0.1-2 Index]