Nothing
if (interactive()) savehistory();
library("aroma.affymetrix");
log <- Verbose(threshold=-10, timestamp=TRUE);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Settings
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
naVersion <- "30";
genomeVersion <- "hg18";
user <- "HB";
datestamp <- "20100215";
chipType <- "GenomeWideSNP_6";
cdfTags <- "Full";
nbrOfEnzymes <- 2;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup required annotation files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (!exists("cdf")) {
cdf <- AffymetrixCdfFile$byChipType(chipType, tags=cdfTags);
rm(csvList);
}
print(cdf);
if (!exists("csvList", mode="list")) {
csvList <- list();
tagsList <- c(
main=sprintf(".na%s", naVersion),
# cn=sprintf(".cn.na%s", naVersion)
cn=sprintf(".cn.na%s", as.integer(naVersion))
);
for (key in names(tagsList)) {
tags <- tagsList[[key]];
pathname <- AffymetrixNetAffxCsvFile$findByChipType(chipType, tags=tags);
if (isFile(pathname)) {
csvList[[key]] <- AffymetrixNetAffxCsvFile(pathname);
}
rm(tags);
}
}
print(csvList);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Import UFL from CSV files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
tags <- sprintf("na%s,%s,%s%s", naVersion, genomeVersion, 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, nbrOfEnzymes=nbrOfEnzymes);
}
print(ufl);
for (kk in seq_along(csvList)) {
csv <- csvList[[kk]];
print(csv);
units <- importFrom(ufl, csv, verbose=log);
str(units);
## GenomeWideSNP_6.na30.annot.csv: int [1:934968] 334945 334944 ...
## GenomeWideSNP_6.cn.na30.annot.csv: int [1:945826] 935622 935777 ...
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Update the file footer
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (!exists("srcFileTags", mode="list")) {
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(ufl);
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);
print(ufl);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# WHAT'S NEW:
#
# o na27.1 -> na30
# - No changes.
# o na27 -> na27.1
# - No changes.
# o na26 -> na27
# - No changes.
# o na24 -> na26
# - All changes are for SNP units.
# - There are 6 NspI and 14 StyI changes in SNP fragment lengths,
# which some are only minor.
# - There are 1108 more SNPs that now have missing values.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
ufl <- AromaUflFile$byChipType("GenomeWideSNP_6,Full", tags="na30");
ufl0 <- AromaUflFile$byChipType("GenomeWideSNP_6,Full", tags="na27.1");
x <- summaryOfUnits(ufl);
x0 <- summaryOfUnits(ufl0);
print(x);
## snp cnp affxSnp other total
## enzyme1-only 246080 451191 0 0 697271
## enzyme2-only 160899 0 0 0 160899
## both 522472 494615 0 0 1017087
## missing 2495 20 3022 621 6158
## total 931946 945826 3022 621 1881415
print(x0);
## snp cnp affxSnp other total
## enzyme1-only 246080 451191 0 0 697271
## enzyme2-only 160899 0 0 0 160899
## both 522472 494615 0 0 1017087
## missing 2495 20 3022 621 6158
## total 931946 945826 3022 621 1881415
print(x-x0);
## snp cnp affxSnp other total
## enzyme1-only 0 0 0 0 0
## enzyme2-only 0 0 0 0 0
## both 0 0 0 0 0
## missing 0 0 0 0 0
## total 0 0 0 0 0
# Differences
for (cc in 1:nbrOfColumns(ufl)) {
units <- whichVector(ufl[,cc] != ufl0[,cc], na.rm=TRUE);
if (length(units) > 0) {
df <- cbind(units, ufl[units,cc], ufl0[units,cc],
ufl[units,cc]-ufl0[units,cc]);
colnames(df)[ncol(df)] <- "delta";
print(df);
}
}
# Differences in NAs
for (cc in 1:nbrOfColumns(ufl)) {
units <- whichVector(is.na(ufl[,cc]) != is.na(ufl0[,cc]));
if (length(units) > 0) {
df <- cbind(units, ufl[units,cc], ufl0[units,cc]);
str(df);
}
}
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