Nothing
source("init.R");
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Settings
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
naVersion <- "25";
user <- "HB";
datestamp <- "20080424";
chipType <- "GenomeWideSNP_5";
cdfTags <- "Full,r2";
nbrOfEnzymes <- 2;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup required annotation files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
if (!exists("cdf")) {
cdf <- AffymetrixCdfFile$byChipType(chipType, tags=cdfTags);
rm(csvList);
}
print(cdf);
if (!exists("csvList", mode="list")) {
csvList <- list();
tags <- sprintf(".na%s", naVersion);
csv <- AffymetrixNetAffxCsvFile$byChipType(chipType, tags=tags);
csvList[["main"]] <- csv;
tags <- sprintf(".cn.na%s", naVersion);
csv <- AffymetrixNetAffxCsvFile$byChipType(chipType, tags=tags);
csvList[["CN"]] <- csv;
rm(csv, tags);
}
print(csvList);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Import UFL from CSV files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
tags <- sprintf("na%s,%s%s", naVersion, user, datestamp);
ufl <- NULL;
tryCatch({
ufl <- AromaUflFile$byChipType(getChipType(cdf), tags=tags);
}, error = function(ex) {})
if (is.null(ufl)) {
ufl <- AromaUflFile$allocateFromCdf(cdf, tags=tags, nbrOfEnzymes=nbrOfEnzymes);
}
print(ufl);
for (kk in seq_along(csvList)) {
csv <- csvList[[kk]];
print(csv);
units <- importFrom(ufl, csv, verbose=log);
str(units);
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Statistics
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
x <- summaryOfUnits(ufl, enzymes=c("NspI", "StyI"));
print(x);
## snp cnp affxSnp other total
## enzyme1-only 116979 140099 0 0 257078
## enzyme2-only 74135 1208 0 0 75343
## both 248980 171077 0 0 420057
## missing 60474 104885 3022 69 168450
## total 500568 417269 3022 69 920928
cdf2 <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
tags <- sprintf("na%s,%s%s", naVersion, user);
ufl2 <- AromaUflFile$byChipType(getChipType(cdf2), tags=tags);
units2 <- match(getUnitNames(cdf), getUnitNames(cdf2));
keep <- is.finite(units2);
print(summary(keep));
units <- which(keep);
units2 <- units2[keep];
for (ee in 1:nbrOfEnzymes(ufl))
ufl[units,ee] <- ufl2[units2,ee];
## snp cnp affxSnp other total
## enzyme1-only 129848 148340 0 0 278188
## enzyme2-only 90353 1208 0 0 91561
## both 273682 181097 0 0 454779
## missing 6685 86624 3022 69 96400
## total 500568 417269 3022 69 920928
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