library("R.utils");
library("aroma.light");
dataSet <- "GSE29172"
chipType <- "GenomeWideSNP_6"
if (FALSE) {
## Define CN regions:
rpn <- sprintf("preprocessing/%s/05.defineCopyNumberSegments.R", dataSet)
pn <- system.file(rpn, package="acnr")
file.exists(pn)
source(pn)
str(regDat)
}
datPath <- "wholeGenomeData";
datPath <- Arguments$getReadablePath(datPath);
regPath <- "png/regions"
regPath <- file.path(regPath, dataSet)
regPath <- Arguments$getWritablePath(regPath)
savPath <- "cnRegionData"
savPath <- Arguments$getWritablePath(savPath)
opath <- file.path(savPath, sprintf("%s,ASCRMAv2", dataSet), chipType);
opath <- Arguments$getWritablePath(opath)
path <- file.path(datPath, sprintf("%s,ASCRMAv2", dataSet), chipType);
path <- Arguments$getReadablePath(path);
patt <- "H1395vsBL1395,([0-9]+).rds"
filenames <- list.files(path, pattern=patt)
pathnames <- file.path(path, filenames)
rm(path)
pct <- as.numeric(gsub(patt, "\\1", filenames))
for (kk in seq(along=pct)) {
pathname <- pathnames[kk]
sampleName <- gsub("(.*)\\.rds$", "\\1", filenames[kk])
print(sampleName)
dat <- loadObject(pathname)
dat$posMb <- dat$x/1e6;
rm(pathname)
## run TumorBoost
betaTN <- normalizeTumorBoost(betaT=dat$betaT,betaN=dat$betaN)
muN <- callNaiveGenotypes(dat$betaN)
dat.norm <- cbind(dat, muN, betaTN, b=2*abs(betaTN-1/2))
bkp <- function(pos) abline(v=pos, col=5, lwd=2)
for (rr in 1:nrow(regDat)) {
chr <- regDat[rr, "chr"]
reg <- c(regDat[rr, "begin"], regDat[rr, "end"])
type <- regDat[rr, "type"]
print(type)
datCC <- subset(dat.norm, chromosome==chr)
minR <- reg[1]
maxR <- reg[2]
datRR <- subset(datCC, posMb>minR & posMb<maxR)
str(datRR)
opos <- order(datRR$x)
datRRo <- datRR[opos, ]
datSS <- datRRo[, c("CT", "betaTN", "muN", "betaT", "betaN")]
names(datSS) <- c("c","b","genotype", "bT", "bN")
datSS <- round(datSS, 3)
filename <- sprintf("%s,%s.rds", sampleName, type)
pathname <- file.path(opath, filename)
saveRDS(datSS, file=pathname)
}
}
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