Nothing
library("R.utils");
library("aroma.light");
library("PSCBS")
datPath <- "wholeGenomeData";
datPath <- Arguments$getReadablePath(datPath);
dataSet <- "GSE29172,ASCRMAv2"
chipType <- "GenomeWideSNP_6"
path <- file.path(datPath, dataSet, chipType);
path <- Arguments$getReadablePath(path);
filenames <- list.files(path, pattern="H1395vsBL1395,([0-9]+).rds")
sampleNames <- gsub("(.*)\\.rds$", "\\1", filenames)
pathnames <- file.path(path, filenames)
figPath <- "png"
figPath <- Arguments$getWritablePath(figPath)
figForce <- FALSE;
for (kk in seq(along=pathnames)) {
sampleName <- sampleNames[kk];
print(sampleName)
pathname <- pathnames[kk];
dat <- loadObject(pathname)
dat$posMb <- dat$x/1e6;
rm(pathname)
## run TumorBoost
betaTN <- normalizeTumorBoost(betaT=dat$betaT,betaN=dat$betaN)
muN <- callNaiveGenotypes(dat$betaN)
dat.norm <- cbind(dat, muN, betaTN, b=2*abs(betaTN-1/2))
## some plots
chrs <- sort(unique(dat.norm$chromosome))
for (cc in seq(along=chrs)) {
chr <- chrs[cc]
print(chr)
datCC <- subset(dat.norm, chromosome==chr)
figName <- sprintf("%s,chr%02d,tracks.png", sampleName, chr)
path <- file.path(figPath, "tracks", dataSet)
path <- Arguments$getWritablePath(path);
pathname <- file.path(path, figName)
if (!file.exists(pathname) || figForce) {
png(pathname, width=1200, height=800)
par(mfrow=c(2,1))
plot(CT~posMb, data=datCC, cex=0.2, ylim=c(0,5), pch=19, xlab="position (Mb)", ylab="copy number")
plot(betaTN~posMb, data=datCC, cex=0.2, ylim=c(0,1), pch=19, xlab="position (Mb)", ylab="B allele Fraction")
dev.off()
}
}
figName <- sprintf("%s,C1C2.png", sampleName)
path <- file.path(figPath, "C1C2", dataSet)
path <- Arguments$getWritablePath(path);
pathname <- file.path(path, figName)
if (!file.exists(pathname)) {
fit <- segmentByPairedPSCBS(dat)
png(pathname, width=800, height=800)
plotC1C2(fit)
linesC1C2(fit)
dev.off()
}
}
datCC <- subset(dat, chromosome==10)
str(datCC)
fitCC <- segmentByPairedPSCBS(datCC)
plotC1C2(fit)
linesC1C2(fit)
pointsC1C2(fitCC, col=2)
linesC1C2(fitCC, col=2)
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