getGEOSAGE {SAGElyzer}R Documentation

Automatically downloads SAGE libraries from NCBI

Description

Given an organism name (e.g. human) and a correct url, getGEOSAGE downloads SAGE libraries and stores them in a specified directory

Usage

getGEOSAGE(organism = "human", targetDir = "", quiet = TRUE, url =
"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?")
getFileNames(organism, url)
getSampleId(url)

Arguments

organism A character string for the name of the organism of interests
targetDir A character string for the directory where the downloaded SAGE libraries will be stored
quiet A boolean indicating whether the status message from download.file will be supressed
url A character string for part of the url from which SAGE libraries will be downloaded

Details

getGEOSAGE downloads SAGE libraries from NCBI's GEO site and stores them in a specified directory. The url passed is the location where the cgi resides and will be appended the correct parameters that specifies the content and format of the data file to be downloaded.

The system relies on GPL numbers that differ among organisms to find the correct platform sample ids for files belonging to a given organism. The platform sample ids will then be used to fetch the desired annotation files. getFileNames gets the correct GPL number and getSampleId gets the platform sample ids. parseSAGE parses the downloaded file and stores the data to a specified place.

Value

getFileNames Returns a vector of GPL numbers
getSampleId Returns a vector of platform sample ids

Note

The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide bioinformatics functionalities through R

Author(s)

J. Zhang

References

http://www.ncbi.nlm.nih.gov/geo/query/

See Also

mergeSAGE

Examples

# Since downloading and parsing SAGE libraries are time consuming, the
# example code is inactivated.
## Not run: 
getGEOSAGE(organism = "human", targetDir = "", quiet = TRUE, url =
"http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?")
## End(Not run)  

[Package SAGElyzer version 1.4.2 Index]