clac.PlotSingleArray.R {clac}R Documentation

A function to plot one single array for CLAC result.

Description

A function to plot one single array for CLAC result.

Usage

clac.PlotSingleArray.R(i, NormalResult, clac.result, centromere=NULL, graylevel=0.9)

Arguments

i integer specifying which array to plot
NormalResult result object of function clac.preparenormal.R
clac.result result object of function clac.tumorarray.R
centromere numeric vector specifying the centromere positions. If missing, the default centromere value of human genome will be used.
graylevel numeric value between 0 and 1, specifying the gray level for the background scale lines. 0 for black and 1 for white.

Details

clac.PlotSingleArray.R plot one single 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]