R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.1  (2005-06-20), ISBN 3-900051-07-0

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> ### * <HEADER>
> ###
> attach(NULL, name = "CheckExEnv")
> assign(".CheckExEnv", as.environment(2), pos = length(search())) # base
> ## add some hooks to label plot pages for base and grid graphics
> setHook("plot.new", ".newplot.hook")
> setHook("persp", ".newplot.hook")
> setHook("grid.newpage", ".gridplot.hook")
> 
> assign("cleanEx",
+        function(env = .GlobalEnv) {
+ 	   rm(list = ls(envir = env, all.names = TRUE), envir = env)
+            RNGkind("default", "default")
+ 	   set.seed(1)
+    	   options(warn = 1)
+ 	   delayedAssign("T", stop("T used instead of TRUE"),
+ 		  assign.env = .CheckExEnv)
+ 	   delayedAssign("F", stop("F used instead of FALSE"),
+ 		  assign.env = .CheckExEnv)
+ 	   sch <- search()
+ 	   newitems <- sch[! sch %in% .oldSearch]
+ 	   for(item in rev(newitems))
+                eval(substitute(detach(item), list(item=item)))
+ 	   missitems <- .oldSearch[! .oldSearch %in% sch]
+ 	   if(length(missitems))
+ 	       warning("items ", paste(missitems, collapse=", "),
+ 		       " have been removed from the search path")
+        },
+        env = .CheckExEnv)
> assign("..nameEx", "__{must remake R-ex/*.R}__", env = .CheckExEnv) # for now
> assign("ptime", proc.time(), env = .CheckExEnv)
> grDevices::postscript("clac-Examples.ps")
> assign("par.postscript", graphics::par(no.readonly = TRUE), env = .CheckExEnv)
> options(contrasts = c(unordered = "contr.treatment", ordered = "contr.poly"))
> options(warn = 1)    
> library('clac')
> 
> assign(".oldSearch", search(), env = .CheckExEnv)
> assign(".oldNS", loadedNamespaces(), env = .CheckExEnv)
> cleanEx(); ..nameEx <- "clac.PlotAllArray.R"
> 
> ### * clac.PlotAllArray.R
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: clac.PlotAllArray.R
> ### Title: A function to plot multiple arrays for CLAC result.
> ### Aliases: clac.PlotAllArray.R
> ### Keywords: cluster
> 
> ### ** 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)
Warning in return(fdr = CLAC.result[1, ], RegionMean = CLAC.result[-c(1,  : 
	 multi-argument returns are deprecated
> 
> ############ 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$fdr[i],3), sep=""))
> 
> ############ consensus plot
> clac.PlotConsensus.R(clac.result, chromosome, nucposition,  1:4)
> title(main="Consensus Plot for 4 BAC arrays")
> 
> ############ Plot all arrays
> clac.PlotAllArray.R(NormalResult, clac.result)
> title(main="Plot for all 4 arrays")
> 
> 
> 
> cleanEx(); ..nameEx <- "clac.PlotConsensus.R"
> 
> ### * clac.PlotConsensus.R
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: clac.PlotConsensus.R
> ### Title: A function to make consensus plot for CLAC result.
> ### Aliases: clac.PlotConsensus.R
> ### Keywords: cluster
> 
> ### ** Examples
> 
> library(clac)
> data(BACarray)
> attach(BACarray)
> 
> ############ prepare the normal reference arrays
> NormalResult<-clac.preparenormal.R(DiseaseArray, NormalArray, Normal.Type=rep(0,3), chromosome.number=chromosome, nucleotide.position=nucposition, windowsize=5, targetFDR=0.01, chromosomeOption=FALSE)
> 
> ############ clac on selected tumor arrays
> clac.result<-clac.tumorarray.R(NormalResult, tumorarrayIndex=1:4)
Warning in return(fdr = CLAC.result[1, ], RegionMean = CLAC.result[-c(1,  : 
	 multi-argument returns are deprecated
> 
> ############ Plot for the first arrays
> i<-1
> clac.PlotSingleArray.R(i, NormalResult, clac.result)
> title(main=paste("CLAC Plot for the ", i ,"th BAC array; FDR=", round(clac.result$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")
> 
> 
> 
> cleanEx(); ..nameEx <- "clac.PlotSingleArray.R"
> 
> ### * clac.PlotSingleArray.R
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: clac.PlotSingleArray.R
> ### Title: A function to plot one single array for CLAC result.
> ### Aliases: clac.PlotSingleArray.R
> ### Keywords: cluster
> 
> ### ** 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)
Warning in return(fdr = CLAC.result[1, ], RegionMean = CLAC.result[-c(1,  : 
	 multi-argument returns are deprecated
> 
> ############ 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$fdr[i],3), sep=""))
> 
> ############ consensus plot
> clac.PlotConsensus.R(clac.result, chromosome, nucposition,  1:4)
> title(main="Consensus Plot for 4 BAC arrays")
> 
> ############ Plot all arrays
> clac.PlotAllArray.R(NormalResult, clac.result)
> title(main="Plot for all 4 arrays")
> 
> 
> 
> cleanEx(); ..nameEx <- "clac.preparenormal.R"
> 
> ### * clac.preparenormal.R
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: clac.preparenormal.R
> ### Title: A function to prepare normal reference in CLAC(Cluster Along
> ###   Chromosome) Analysis
> ### Aliases: clac.preparenormal.R
> ### Keywords: cluster
> 
> ### ** Examples
> 
> library(clac)
> data(BACarray)
> attach(BACarray)
> 
> ############ prepare the normal reference arrays
> NormalResult<-clac.preparenormal.R(DiseaseArray, NormalArray, Normal.Type=rep(0,3), chromosome.number=chromosome, nucleotide.position=nucposition, windowsize=5, targetFDR=0.01, chromosomeOption=FALSE)
> 
> ############ clac on selected tumor arrays
> clac.result<-clac.tumorarray.R(NormalResult, tumorarrayIndex=1:4)
Warning in return(fdr = CLAC.result[1, ], RegionMean = CLAC.result[-c(1,  : 
	 multi-argument returns are deprecated
> 
> ############ Plot for the first arrays
> i<-1
> clac.PlotSingleArray.R(i, NormalResult, clac.result)
> title(main=paste("CLAC Plot for the ", i ,"th BAC array; FDR=", round(clac.result$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")
> 
> 
> 
> cleanEx(); ..nameEx <- "clac.tumorarray.R"
> 
> ### * clac.tumorarray.R
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: clac.tumorarray.R
> ### Title: A function to do CLAC(Cluster Along Chromosome) Analysis
> ### Aliases: clac.tumorarray.R
> ### Keywords: cluster
> 
> ### ** 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)
Warning in return(fdr = CLAC.result[1, ], RegionMean = CLAC.result[-c(1,  : 
	 multi-argument returns are deprecated
> 
> ############ 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")
> 
> 
> 
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", env = .CheckExEnv),"\n")
Time elapsed:  29.65 4.29 34.32 0 0 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')