library(oligo);
fullFilenames <- list.celfiles(path = "/storage/data/elf/MBra/teste", full.names = TRUE);
outputDir     <- file.path(getwd(), "crlmmTest");

crlmm(fullFilenames, outputDir, verbose = FALSE);
crlmmOut <- getCrlmmSummaries(outputDir);

library(DNAcopy)
grps <- rep(c('normal', 'tumor'), each=7)

theS <- getA(crlmmOut) * 2



colnames(theS) <- paste(grps, 1:7, sep='')

library(pd.mapping250k.nsp)
snpInfo <- dbGetQuery(db(pd.mapping250k.nsp), 'SELECT man_fsetid, chrom, physical_pos FROM featureSet WHERE man_fsetid LIKE "SNP%"')
i <- match(rownames(theS), snpInfo[['man_fsetid']])
theS <- theS[i]



logRatioSense <- theS[, 8:14, 2]-theS[, 1:7, 2]
logRatioAntisense <- theS[, 8:14, 1]-theS[, 1:7, 1]

cnObjSense <- CNA(logRatioSense, chrom=snpInfo[["chrom"]], maploc=snpInfo[["physical_pos"]], data.type="logratio")

smoothedCNASense <- smooth.CNA(cnObjSense)

segment.smoothed.CNA.object <- segment(smoothedCNASense)

sdundo.CNA.object <- segment(smoothedCNASense, undo.splits = "sdundo",undo.SD = 3, verbose = 1)

pdf("mainResults.pdf")

plot(segment.smoothed.CNA.object, plot.type='s')
plot(segment.smoothed.CNA.object, plot.type='w')
plot(sdundo.CNA.object, plot.type='s')

dev.off()