clac.PlotConsensus.R {clac}

A function to make consensus plot for CLAC result.

Package:

clac

Version:

0.1-1

Description

A function to make consensus plot for CLAC result.

Usage

clac.PlotConsensus.R(clac.result, chromosome.number, nucleotide.position, sample.index, centromere=NULL,graylevel=0.9)

Arguments

clac.result: Result object of function clac.tumorarray.R
chromosome.number: numeric vector . Length should be the same as the row number of NORMAL. It's the chromosome number of each gene/clone.
nucleotide.position: numeric vector. Length should be the same as the row number of NORMAL. It's the nucleotide position of each gene/clone.
sample.index: integer vector. It's the index of the arrays to be included in the consensus plot.
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.PlotConsensus.R make consensus plot for CLAC result.

Values

No return value.

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")

Author(s)

Pei Wang

Documentation reproduced from package clac, version 0.1-1. License: GPL (>= 2)