Nothing
if (interactive()) savehistory();
library("aroma.affymetrix");
library("R.menu");
verbose <- Verbose(threshold=-10, timestamp=TRUE);
options(width=60);
chipType <- "Mapping50K_Hind240";
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# User settings
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
## setOption(aromaSettings, "user/initials", "HB");
## setOption(aromaSettings, "user/fullname", "Henrik Bengtsson");
## email <- sprintf("%s@%s", "henrik.bengtsson", "aroma-project.org")
## setOption(aromaSettings, "user/email", email);
## saveAnywhere(aromaSettings);
fullname <- getOption(aromaSettings, "user/fullname");
stopifnot(!is.null(fullname));
email <- getOption(aromaSettings, "user/email");
stopifnot(!is.null(email));
user <- getOption(aromaSettings, "user/initials");
stopifnot(!is.null(user));
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Settings
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
genomeVersions <- c("30"="hg18", "31"="hg19");
naVersions <- names(genomeVersions);
choices <- sprintf("na%s (%s)", naVersions, genomeVersions);
choice <- textMenu(choices, title="Choose NetAffx version: ", value=FALSE);
naVersion <- naVersions[choice];
genomeVersion <- genomeVersions[naVersion];
datestamp <- format(Sys.Date(), format="%Y%m%d");
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup required annotation files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cdf <- AffymetrixCdfFile$byChipType(chipType);
print(cdf);
tags <- sprintf(".na%s", naVersion);
pathname <- AffymetrixNetAffxCsvFile$findByChipType(chipType, tags=tags);
if (isFile(pathname)) {
csv <- AffymetrixNetAffxCsvFile(pathname);
}
rm(tags);
print(csv);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Import UGP from CSV files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
tags <- sprintf("na%s,%s,%s%s", naVersion, genomeVersion, user, datestamp);
ugp <- NULL;
tryCatch({
ugp <- AromaUgpFile$byChipType(getChipType(cdf), tags=tags);
}, error = function(ex) {})
if (is.null(ugp)) {
ugp <- AromaUgpFile$allocateFromCdf(cdf, tags=tags);
}
print(ugp);
units <- importFrom(ugp, csv, verbose=verbose);
str(units);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Update the file footer
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
srcFileTags <- list();
srcFiles <- list(cdf, csv);
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(ugp);
footer$createdOn <- format(Sys.time(), "%Y%m%d %H:%M:%S", usetz=TRUE);
footer$createdBy = list(
fullname = fullname,
email = email
);
names(srcFileTags) <- sprintf("srcFile%d", seq_along(srcFileTags));
footer$srcFiles <- srcFileTags;
writeFooter(ugp, footer);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Statistics
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
print(ugp);
print(summary(ugp));
print(table(ugp[,1]));
## Mapping50K_Hind240,na31,hg19,HB20110328
## 1 2 3 4 5 6 7 8 9 10 11 12
## 4537 5067 3959 4339 4213 3946 3447 3546 2356 2740 2464 2589
## 13 14 15 16 17 18 19 20 21 22 23 24
## 2646 1931 1439 1142 985 1730 324 992 879 430 1160 1
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