library("R.utils");
dataSet <- "GSE13372"
if (FALSE) {
## Define CN regions
regFile <- "05.defineCopyNumberSegments.R"
pn <- file.path("preprocessing", dataSet, regFile)
sf <- system.file(pn, package="acnr")
source(sf)
str(regDat)
}
datPath <- "wholeGenomeData";
datPath <- Arguments$getReadablePath(datPath);
dataSet <- "GSE13372,ASCRMAv2"
chipType <- "GenomeWideSNP_6"
path <- file.path(datPath, dataSet, chipType);
path <- Arguments$getReadablePath(path);
filenames <- list.files(path, pattern="HCC1143_GLEYSvsHCC1143BL_GLEYS,([0-9]+).rds")
sampleNames <- gsub("(.*)\\.rds$", "\\1", filenames)
pathnames <- file.path(path, filenames)
for (kk in seq(along=filenames)) {
filename <- filenames[kk]
sampleName <- gsub("(.*)\\.rds$", "\\1", filename)
pathname <- file.path(path, filename)
print(sampleName)
pathname <- pathnames[kk];
dat <- readRDS(pathname)
dat$posMb <- dat$x/1e6;
rm(pathname)
## run TumorBoost
muN <- aroma.light::callNaiveGenotypes(dat$betaN)
gens <- table(muN, exclude = NULL)
stopifnot(all(c("0", "0.5", "1") %in% names(gens))) ## sanity check: are all genotypes represented?
betaTN <- aroma.light::normalizeTumorBoost(betaT=dat$betaT,betaN=dat$betaN, muN=muN)
dat.norm <- cbind(dat, muN, betaTN, b=2*abs(betaTN-1/2))
regPath <- "png/regions"
regPath <- file.path(regPath, dataSet)
regPath <- Arguments$getWritablePath(regPath)
savPath <- "cnRegionData"
savPath <- Arguments$getWritablePath(savPath)
path <- file.path(savPath, dataSet, chipType);
path <- Arguments$getWritablePath(path)
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)
datRR <- subset(datCC, posMb>reg[1] & posMb<reg[2])
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(path,filename)
saveRDS(datSS, file=pathname)
}
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.