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, srcUrls = getSrcUrl("all", organism), otherSrc = NULL, baseMapType = c("gbNRef", "gb", "ug", "ll"), version = "1.1.0", fromWeb = TRUE, baseUrl = "ftp://ftp.tigr.org/pub/data/tgi/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 |
srcUrls |
srcUrls a vector of names character strings for
the urls where source data files are retained. Valid sources are
LocusLink, UniGene, Golden Path, Gene Ontology, and KEGG. The names
for the character strings should be LL, UG, GP, GO, and KEGG,
respectively. LL and UG are required |
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 |
otherSrc |
otherSrc a vector of named character strings
for the names of files that contain mappings between probe ids of
baseName and LocusLink ids that will be used to obtain the unified
mappings between probe ids of baseName and LocusLink ids based on
all the sources. The strings should not contain any number and the
files have the same structure as baseName |
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 |
fromWeb |
fromWeb a boolean indicating whether source
files used to build a data package will be obtained on line |
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.
This function is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R
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) }