biocLite("crlmm")
biocLite("genomewidesnp6Crlmm")
biocLite("hapmapsnp6")


if (require(genomewidesnp6Crlmm) & require(hapmapsnp6)){
  path <- system.file("celFiles", package="hapmapsnp6")

  ## the filenames with full path...
  ## very useful when genotyping samples not in the working directory
  cels <- list.celfiles(path, full.names=TRUE)
  (crlmmOutput <- crlmm(cels))
}

## accessors

##genotype calls
str(calls(crlmmOutput))

## smoothing copy number with CBS
biocLite("DNAcopy")

## follow the vignette
library(DNAcopy)
## load in data and explore
data(coriell)
head(coriell)
## number of clones on each chromosome
table(coriell$Chromosome)

## make a CNA object and smooth
CNA.object <- CNA(cbind(coriell$Coriell.05296), coriell$Chromosome,
                  coriell$Position, data.type = "logratio", sampleid = "c05296")
smoothed.CNA.object <- smooth.CNA(CNA.object)
## segmentation
segment.smoothed.CNA.object <- segment(smoothed.CNA.object, verbose = 1)
## plot it
plot(segment.smoothed.CNA.object, plot.type = "w")
## plot by chromosome
plot(segment.smoothed.CNA.object, plot.type = "s")

plot(segment.smoothed.CNA.object, plot.type = "p")

## remove small change points
sdundo.CNA.object <- segment(smoothed.CNA.object, undo.splits = "sdundo",
                             undo.SD = 3, verbose = 1)
plot(sdundo.CNA.object, plot.type = "s")
## change points in chr4 and 21 are removed