Nothing
if (interactive()) savehistory();
library("aroma.affymetrix");
library("R.menu");
verbose <- Verbose(threshold=-10, timestamp=TRUE);
options(width=60);
chipType <- "Mapping50K_Xba240";
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# User settings
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
## setOption(aromaSettings, "user/initials", "HB");
## setOption(aromaSettings, "user/fullname", "Henrik Bengtsson");
## email <- sprintf("%s@%s", "henrik.bengtsson", "aroma-project.org")
## setOption(aromaSettings, "user/email", email);
## 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");
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$byChipType(chipType);
print(cdf);
tags <- sprintf(".na%s", naVersion);
pathname <- AffymetrixNetAffxCsvFile$findByChipType(chipType, tags=tags);
if (isFile(pathname)) {
csv <- AffymetrixNetAffxCsvFile(pathname);
}
rm(tags);
print(csv);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Import UGP from CSV files
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
tags <- sprintf("na%s,%s,%s%s", naVersion, genomeVersion, user, datestamp);
ugp <- NULL;
tryCatch({
ugp <- AromaUgpFile$byChipType(getChipType(cdf), tags=tags);
}, error = function(ex) {})
if (is.null(ugp)) {
ugp <- AromaUgpFile$allocateFromCdf(cdf, tags=tags);
}
print(ugp);
units <- importFrom(ugp, csv, verbose=verbose);
str(units);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Update the file footer
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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(ugp);
footer$createdOn <- format(Sys.time(), "%Y%m%d %H:%M:%S", usetz=TRUE);
footer$createdBy = list(
fullname = fullname,
email = email
);
names(srcFileTags) <- sprintf("srcFile%d", seq_along(srcFileTags));
footer$srcFiles <- srcFileTags;
writeFooter(ugp, footer);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Statistics
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
print(ugp);
print(summary(ugp));
print(table(ugp[,1]));
## AromaUgpFile:
## Name: Mapping50K_Xba240
## Tags: na31,hg19,HB20110328
## Full name: Mapping50K_Xba240,na31,hg19,HB20110328
## Pathname: annotationData/chipTypes/Mapping50K_Xba240/Mapping50K_Xba240,na31,hg19
## ,HB20110328.ugp
## File size: 288.77 kB (295699 bytes)
## RAM: 0.01 MB
## Number of data rows: 59015
## File format: v1
## Dimensions: 59015x2
## Column classes: integer, integer
## Number of bytes per column: 1, 4
## Footer: <createdOn>20110328 18:46:23 PDT</createdOn><platform>Affymetrix</platfo
## rm><chipType>Mapping50K_Xba240</chipType><createdBy><fullname>Henrik Bengtsson</
## fullname><email>[...]</email></createdBy><srcFiles><srcFile1><fil
## ename>Mapping50K_Xba240.CDF</filename><filesize>57703961</filesize><checksum>7f0
## 26f6472f7721255717fb3f453be61</checksum></srcFile1><srcFile2><filename>Mapping50
## K_Xba240.na31.annot.csv</filename><filesize>84705402</filesize><checksum>4cc4997
## 35dd13177331994cde4e9f323</checksum></srcFile2></srcFiles>
## Chip type: Mapping50K_Xba240
## Platform: Affymetrix
##
## chromosome position
## Min. : 1.000 Min. : 110819
## 1st Qu.: 4.000 1st Qu.: 35046332
## Median : 7.000 Median : 72991749
## Mean : 8.504 Mean : 80414591
## 3rd Qu.: 12.000 3rd Qu.:114933994
## Max. : 24.000 Max. :248818466
## NA's :485.000 NA's : 485
##
## 1 2 3 4 5 6 7 8 9 10 11 12
## 4662 5271 3863 4227 4141 4094 3609 3422 2436 2948 2892 2684
## 13 14 15 16 17 18 19 20 21 22 23 24
## 2555 2081 1587 1238 968 1835 363 1100 1023 326 1203 2
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