Nothing
library("aroma.affymetrix")
verbose <- Verbose(threshold=-10, timestamp=TRUE)
options(width=60)
chipType <- "GenomeWideSNP_6"
cdfTags <- "Full"
nbrOfEnzymes <- 2
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# User settings
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
fullname <- "Henrik Bengtsson"
user <- "HB"
email <- getOption(aromaSettings, "user/email")
if (is.null(email)) {
email <- "JohnDoe@email.com"
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Settings
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
naVersion <- "32"
genomeVersion <- "hg19"
datestamp <- format(Sys.Date(), format="%Y%m%d")
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup required annotation files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cdf <- AffymetrixCdfFile$byChipType(chipType, tags=cdfTags)
print(cdf)
csvList <- list()
tagsList <- c(
main=sprintf(".na%s", naVersion),
cn=sprintf(".cn.na%s", naVersion)
)
for (key in names(tagsList)) {
tags <- tagsList[[key]]
pathname <- AffymetrixNetAffxCsvFile$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)
tags <- c("TEST-ONLY", tags)
ufl <- AromaUflFile$allocateFromCdf(cdf, tags=tags, nbrOfEnzymes=nbrOfEnzymes, overwrite=TRUE)
print(ufl)
for (kk in seq_along(csvList)) {
csv <- csvList[[kk]]
print(csv)
units <- importFrom(ufl, csv, verbose=verbose)
str(units)
## GenomeWideSNP_6.na<XX>.annot.csv: int [1:934968] 334945 334944 ...
## GenomeWideSNP_6.cn.na<XX>.annot.csv: int [1:945826] 935622 935777 ...
}
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Update the file footer
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
srcFileTags <- list()
srcFiles <- c(list(cdf), csvList)
for (kk in seq_along(srcFiles)) {
srcFile <- srcFiles[[kk]]
tags <- list(
filename=getFilename(srcFile),
filesize=getFileSize(srcFile),
checksum=getChecksum(srcFile)
)
srcFileTags[[kk]] <- tags
}
print(srcFileTags)
footer <- readFooter(ufl)
footer$createdBy <- list(
fullname = fullname,
email = email
)
names(srcFileTags) <- sprintf("srcFile%d", seq_along(srcFileTags))
footer$srcFiles <- srcFileTags
writeFooter(ufl, footer)
# Try to load the created annotation file
ufl <- AromaUflFile$byChipType("GenomeWideSNP_6,Full", tags="TEST-ONLY")
print(ufl)
x <- summaryOfUnits(ufl)
print(x)
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