library("aroma.cn");
library("PSCBS");
library("R.devices");
library("R.menu");
verbose <- Arguments$getVerbose(-10);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup Paired PSCBS segmentation data set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
rootPath <- "pscbsData";
path <- Arguments$getReadablePath(rootPath);
dataSets <- list.files(rootPath);
if (length(dataSets) > 1) {
dataSet <- textMenu(dataSets, value=TRUE);
} else {
dataSet <- dataSets[1];
}
path <- file.path(rootPath, dataSet);
path <- Arguments$getReadablePath(path);
chipTypes <- list.files(path);
if (length(chipTypes) > 1) {
chipType <- textMenu(chipTypes, value=TRUE);
} else {
chipType <- chipTypes[1];
}
ds <- PairedPSCBSFileSet$byName(dataSet, chipType=chipType);
print(ds);
dsName <- getName(ds);
if (length(ds) == 0) {
throw("No PairedPSCBS data file found.")
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Select tumor-normal pair
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (length(ds) > 1) {
ii <- textMenu(getFullNames(ds));
} else {
ii <- 1L;
}
df <- getFile(ds, ii);
fit <- loadObject(df);
sampleName <- getFullName(df);
sampleName <- gsub(",PairedPSCBS", "", sampleName, fixed=TRUE);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# REPORT
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
tryCatch({
report(fit, rspTags="deShear", sampleName=sampleName, studyName=dataSet, force=TRUE);
}, error=function(ex) {
.lastError <<- ex;
});
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