if (interactive()) savehistory();
library("aroma.affymetrix");
log <- Verbose(threshold=-50, timestamp=TRUE);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Settings
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
naVersion <- "26";
user <- "HB";
datestamp <- "20080916";
chipType <- "Mapping250K_Nsp";
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup required annotation files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (!exists("cdf")) {
cdf <- AffymetrixCdfFile$byChipType(chipType);
rm(csv);
}
print(cdf);
if (!exists("csv")) {
tags <- sprintf(".na%s", naVersion);
pathname <- AffymetrixNetAffxCsvFile$findByChipType(chipType, tags=tags);
if (isFile(pathname)) {
csv <- AffymetrixNetAffxCsvFile(pathname);
}
rm(tags);
}
print(csv);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Import UFL from CSV files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
tags <- sprintf("na%s,%s%s", naVersion, user, datestamp);
ufl <- NULL;
tryCatch({
ufl <- AromaUflFile$byChipType(getChipType(cdf), tags=tags);
}, error = function(ex) {})
if (is.null(ufl)) {
ufl <- AromaUflFile$allocateFromCdf(cdf, tags=tags);
}
print(ufl);
enzyme <- gsub("Mapping250K_(Nsp|Sty)", "\\1I", getChipType(ufl));
print(enzyme);
stopifnot(nchar(enzyme) == 4);
units <- importFrom(ufl, csv, enzymes=enzyme, verbose=log);
str(units);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Update the file footer
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (!exists("srcFileTags", mode="list")) {
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(ufl);
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;
writeFooter(ufl, footer);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Statistics
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
print(ufl);
x <- summaryOfUnits(ufl);
print(x);
## AromaUflFile:
## Name: Mapping250K_Nsp
## Tags: na26,HB20080916
## Pathname: annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp,na26,HB20080916.ufl
## File size: 512.98kB
## RAM: 0.00MB
## Number of data rows: 262338
## File format: v1
## Dimensions: 262338x1
## Column classes: integer
## Number of bytes per column: 2
## Footer: <platform>Affymetrix</platform><chipType>Mapping250K_Nsp</chipType><createdOn>20080916 17:23:12 PDT</createdOn><createdBy><fullname>Henrik Bengtsson</fullname><email>[...]</email></createdBy><srcFiles><srcFile1><filename>Mapping250K_Nsp.cdf</filename><filesize>194455495</filesize><checksum>59ae263311a2cf63b8d1b9b4cc7d663b</checksum></srcFile1><srcFile2><filename>Mapping250K_Nsp.na26.annot.csv</filename><filesize>447194757</filesize><checksum>5f651b351a0d97e5e9e657f123e6ed05</checksum></srcFile2></srcFiles>
## Chip type: Mapping250K_Nsp
## Platform: Affymetrix
## snp cnp affxSnp other total
## enzyme1-only 261563 0 0 0 261563
## missing 701 0 0 74 775
## total 262264 0 0 74 262338
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