Nothing
library("ACNE");
verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
dataSet <- "Affymetrix_2006-TumorNormal";
chipType <- "Mapping250K_Nsp";
res <- doACNE(dataSet, chipType=chipType, verbose=verbose);
print(res);
ds <- res$total;
dfR <- getAverageFile(ds, verbose=verbose);
df <- getFile(ds, 1);
baf <- getFile(res$fracB, 1);
ugp <- getAromaUgpFile(ds);
fig <- sprintf("%s", getFullName(df));
if (!devIsOpen(fig)) {
devSet(fig, width=10, height=5);
subplots(2*3, nrow=2, byrow=FALSE);
par(mar=c(3,4,2,1)+0.1, pch=".");
for (chr in 1:3) {
units <- getUnitsOnChromosome(ugp, chr);
pos <- getPositions(ugp, units=units);
beta <- extractMatrix(baf, units=units, drop=TRUE);
fracB <- RawAlleleBFractions(beta, pos, chromosome=chr);
theta <- extractMatrix(df, units=units, drop=TRUE);
thetaR <- extractMatrix(dfR, units=units, drop=TRUE);
C <- 2 * theta/thetaR;
cn <- RawCopyNumbers(C, pos, chromosome=chr);
plot(cn, col="gray", cex=0.8, ylim=c(0,4));
xOut <- seq(xMin(cn), xMax(cn), by=0.5e6);
cnS <- gaussianSmoothing(cn, xOut=xOut, sd=1e6);
points(cnS, col="black");
stext(side=3, pos=0, getName(df));
stext(side=3, pos=1, sprintf("Chr%d", chr));
plot(fracB, ylim=c(0,1));
box(col="blue");
stext(side=3, pos=0, getTags(ds, collapse=","));
stext(side=3, pos=1, sprintf("Chr%d", chr));
} # for (chr ...)
devDone();
}
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