Nothing
if (interactive()) savehistory();
library("aroma.affymetrix");
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Allocate UGC file
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
ugc <- AromaUnitGcContentFile$allocateFromCdf(cdf, tags="na27,h=500kb,HB20090322");
print(ugc);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Import GC contents from NetAffx files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
csvList <- list(
AffymetrixNetAffxCsvFile$byChipType("GenomeWideSNP_6", tags=".cn.na27"),
AffymetrixNetAffxCsvFile$byChipType("GenomeWideSNP_6", tags=".na27.1")
);
colClasses <- c("^(probeSetID|%GC)$"="character");
for (csv in csvList) {
data <- readDataFrame(csv, colClasses=colClasses);
units <- indexOf(cdf, names=data$probeSetID);
ugc[units,1] <- as.double(data[["%GC"]]);
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Update the file footer
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
srcFileTags <- list();
srcFiles <- c(list(cdf), csvList);
for (kk in seq_along(srcFiles)) {
srcFile <- srcFiles[[kk]];
tags <- list(
filename=getFilename(srcFile),
filesize=getFileSize(srcFile),
checksum=getChecksum(srcFile)
);
srcFileTags[[kk]] <- tags;
}
print(srcFileTags);
footer <- readFooter(ugc);
footer$createdOn <- format(Sys.time(), "%Y%m%d %H:%M:%S", usetz=TRUE);
footer$createdBy = list(
fullname = "Henrik Bengtsson",
email = sprintf("%s@%s", "henrik.bengtsson", "aroma-project.org")
);
names(srcFileTags) <- sprintf("srcFile%d", seq_along(srcFileTags));
footer$srcFiles <- srcFileTags;
footer$gcBinWidth <- as.integer(500e3);
writeFooter(ugc, footer);
print(ugc);
print(summary(ugc));
print(range(ugc[,1]));
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