library(DNAcopy)

data(coriell)

#Vytvorime objekt pre jednu vzorku
CNA.object <- CNA(cbind(coriell$Coriell.05296),
                  coriell$Chromosome,
                  coriell$Position, 
                  data.type="logratio",sampleid="c05296")

#Vyhladime jednobodove odlahle pozorovania
smoothed.CNA.object <- smooth.CNA(CNA.object)

#Detekujeme segmenty
segment.smoothed.CNA.object <- segment(smoothed.CNA.object, verbose=1)

head(segment.smoothed.CNA.object$data)
head(segment.smoothed.CNA.object$output)
# stlpce zlava do prava: oznacenie vzorky, cislo chromozomu, 
#zaciatok segmentu, koniec segmentu, pocet sond v danej oblasti, 
#primerny pomer v danej oblasti

head(segment.smoothed.CNA.object$segRows)
# zaciatky a konce segmentov v datach
head(segment.smoothed.CNA.object$call)

segments.summary(segment.smoothed.CNA.object)



##Vyzualizacia vysledkov
# vsetky chromozomy
plot(segment.smoothed.CNA.object, plot.type="w")

# po chromozomoch
plot(segment.smoothed.CNA.object, plot.type="s")

#usporiadane podla priemeru
plot(segment.smoothed.CNA.object, plot.type="p")

# analyza viac vzoriek
CNA.object <- CNA(cbind(coriell$Coriell.05296,coriell$Coriell.13330),
                  coriell$Chromosome,coriell$Position,
                  data.type="logratio",sampleid=c("c05296","c13330"))

smoothed.CNA.object <- smooth.CNA(CNA.object)
segment.smoothed.CNA.object <- segment(smoothed.CNA.object, verbose=1)

plot(segment.smoothed.CNA.object, plot.type="c", cbys.layout=c(2,1), cbys.nchrom=6)

# vynechanie segmentov s malou odchylkou
sdundo.CNA.object <- segment(smoothed.CNA.object,
                             undo.splits="sdundo",
                             undo.SD=3,verbose=1)

plot(sdundo.CNA.object,plot.type="s")