clac.tumorarray.R {clac}

A function to do CLAC(Cluster Along Chromosome) Analysis

Package:

clac

Version:

0.1-1

Description

A function to do CLAC(Cluster Along Chromosome) Analysis

Usage

clac.tumorarray.R(NormalResult, tumorarrayIndex)

Arguments

NormalResult: result object from function clac.preparenormal.R in package clac.
tumorarrayIndex: a vector serving as a subscript index to take out a subset of the disease arrays for analysis

Details

clac.tumorarray.R do CLAC analysis on selected arrays.

Values

A list with components

RegionMean: data matrix reporting the CLAC result. It has the same dimension as the original input data matrix CANCER of function clac.preparenormal.R. For each entry of the matrix, 0 is reported if this genes/clone is not being called to have any copy number alteration, otherwise the amplificaiton/deletion region mean of the genes/clone is reported.
fdr: numeric vector reporting the result FDR for each target disease array.

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)