resourcerer2BioC {Resourcerer} | R Documentation |
TIGR Resourcerer maintains various annotation files for Affymetrix or cDNA chips. This function allows users to create a bioC annotation data package for the probes contained in the Resourcerer annotation file.
resourcerer2BioC(which, organism = c("human", "mouse", "rat"), destDir = file.path(.path.package("Resourcerer"), "temp"), pkgName, pkgPath, baseMapType = c("gbNRef", "gb", "ug", "ll"), version = "1.1.0", baseUrl = "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer", check = FALSE, author = list(authors = "Anonymous", maintainer = "Anonymous <anonymous@email.com>"), exten = "zip")
which |
which a character string indicating which
Resourcerer annotation file to be read in |
destDir |
destDir a character string for the path of a
directory where the downloaded file will be stored. If missing, the
temp directory will be the default |
baseUrl |
baseUrl a character string for the url of
Resourcerer ftp site where directories containing annotation files
for human, rat, mouse ... are stored |
baseMapType |
baseMapType a character string that is
either "gb","ug", or "ll" to indicate whether the probe ids in
baseName are mapped to GenBack accession numbers, UniGene ids, or
LocusLink ids |
pkgName |
pkgName a character string for the name of the
data package to be built (e. g. hgu95a, rgu34a) |
pkgPath |
pkgPath a character string for the full path of
an existing directory where the built backage will be stored |
organism |
organism a character string for the name of the
organism of concern (now can only be "human", "mouse", or "rat") |
version |
version a character string for the version number |
author |
author a list of character strings with an author
element for the name of the author and maintainer element for the
email address of the author |
check |
check a boolean incicating whether to check the
mappings between probe ids and LocusLink ids obtained from Resourcer
and bioC AnnBuilder when baseMapType is 'll' |
exten |
exten a character string for the extension
(e. g. zip) of the source data file to be processed |
baseUrl
is the root directory of TIGR ftp site for Resourcerer
that contains subdirectories holding data for different organism.
Function resourcerer2BioC returns invisible() if successfully executed.
Jianhua Zhang
http://pga.tigr.org/tigr-scripts/magic/r1.pl
############################################################# ## The example takes a loooong time (about an hour) to run ## ############################################################# if(interactive()){ resourcerer2BioC("Agilent_Human1_cDNA.zip", baseMapType = "gbNRef") unlink(file.path(.path.package("Resourcerer"), "temp", "AgilentHuman1cDNA"), TRUE) }