getRsourcerer: A function that downloads an annotation file from TIGR...
TIGR Resourcerer maintains various annotation files for Affymetrix or
cDNA chips. This function allows users to read an annotation file into R
as a matrix.
getResourcerer(which, organism, destDir =
file.path(path.package("Resourcerer"), "temp"), baseUrl = "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer", clean = TRUE, exten = "zip")
which a character string indicating which
annotation file to be read in. The annotation files are stored in
subdirectories for various organisms under
organism a character string for the name of the
organism of interests
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 a character string for the url of
Resourcerer ftp site where directories containing annotation files
for human, rat, mouse ... are stored
clean a boolean indicating whether the file
downloaded from Resourcerer will be removed after the data contained
have been read in
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 getResourcerer returns a matrix derived from the source
data. Column names of the returned matrix are taken directly from the
source file provided by Resourcerer. Users are advised to visit the
Resourcerer web site for more information about the source data files.
resourcerer <- getResourcerer("Agilent_Human1_cDNA.zip", organism = "human",
destDir = file.path(path.package("Resourcerer"), "temp"),
baseUrl = "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data/Resourcerer",
clean = TRUE, exten = "zip")