getResourcerer {Resourcerer} | R Documentation |
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 = c("human", "mouse", "rat"), destDir = file.path(.path.package("Resourcerer"), "temp"), baseUrl = "ftp://ftp.tigr.org/pub/data/tgi/Resourcerer", clean = TRUE, exten = "zip")
which |
which a character string indicating which
annotation file to be read in. The annotation files are stored in
subdirectories for various organisms under baseUrl (see
below) |
organism |
organism a character string for the name of the
organism of interests (has to be either human, mouse, or rat) |
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 |
clean |
clean a boolean indicating whether the file
downloaded from Resourcerer will be removed after the data contained
have been read in |
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 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.
This function is part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalitier through R
Jianhua Zhang
http://pga.tigr.org/tigr-scripts/magic/r1.pl
resourcerer <- getResourcerer("Agilent_Human1_cDNA.zip", organism = "human", destDir = file.path(.path.package("Resourcerer"), "temp"), baseUrl = "ftp://ftp.tigr.org/pub/data/tgi/Resourcerer", clean = TRUE, exten = "zip") resourcerer[1:3,]