A function that downloads an annotation file from TIGR Resourcerer and then read the downloaded file in as a matrix

Share:

Description

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.

Usage

1
2
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")  

Arguments

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

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

Details

baseUrl is the root directory of TIGR ftp site for Resourcerer that contains subdirectories holding data for different organism.

Value

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.

Author(s)

Jianhua Zhang

References

http://pga.tigr.org/tigr-scripts/magic/r1.pl

See Also

"resourcerer2BioC"

Examples

1
2
3
4
5
  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")
  resourcerer[1:3, ]