inst/buildScripts/chipTypes/CytoScanHD_Array/na32/CytoScanHD_Array,UFL.R

In aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

if (interactive()) savehistory();
library("aroma.affymetrix");
library("R.menu");
verbose <- Verbose(threshold=-10, timestamp=TRUE);
options(width=60);

chipType <- "CytoScanHD_Array";
nbrOfEnzymes <- 1;


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
# User settings
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
## setOption(aromaSettings, "user/initials", "HB");
## setOption(aromaSettings, "user/fullname", "Henrik Bengtsson");
## obf <- sprintf("%s@%s", "henrik.bengtsson", "aroma-project.org");
## setOption(aromaSettings, "user/email", obf);
## saveAnywhere(aromaSettings);
setOption(aromaSettings, "user/initials", "HB");
setOption(aromaSettings, "user/fullname", "Henrik Bengtsson");
obf <- sprintf("%s@%s", "henrik.bengtsson", "aroma-project.org");
setOption(aromaSettings, "user/email", obf);
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", "32"="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);
rm(csvList);
print(cdf);

csvList <- list();

tagsList <- c(
  main=sprintf(".na%s", naVersion),
  cn=sprintf(".cn.na%s", 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=verbose);
  str(units);
  ## CytoScanHD_Array.na<XX>.annot.csv:  int [1:?] ? ? ...
  ## CytoScanHD_Array.cn.na<XX>.annot.csv: int [1:2020591] 2116816 1458524
}


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
# 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(ufl);
footer$createdBy <- list(
  fullname = fullname, 
  email = email
);
names(srcFileTags) <- sprintf("srcFile%d", seq_along(srcFileTags));
footer$srcFiles <- srcFileTags;
writeFooter(ufl, footer);

print(ufl);


# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
# WHAT'S NEW:
#
# o na32
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
ufl <- AromaUflFile$byChipType(chipType, tags="na32");
x <- summaryOfUnits(ufl);

print(x);

## CytoScanHD_Array,na32,hg19,HB20111108.ufl
             snp cnp affxSnp   other   total
enzyme1-only   0   0       0 2819458 2819458
missing        0   0       0    2667    2667
total          0   0       0 2822125 2822125

stop()

# 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);
  }
}