clac.PlotConsensus.R {clac} | R Documentation |
A function to make consensus plot for CLAC result.
clac.PlotConsensus.R(clac.result, chromosome.number, nucleotide.position, sample.index, centromere=NULL,graylevel=0.9)
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. |
clac.PlotConsensus.R
make consensus plot for CLAC result.
No return value.
Pei Wang
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/
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")