getGEOSAGE {SAGElyzer} | R Documentation |
Given an organism name (e.g. human) and a correct url,
getGEOSAGE
downloads SAGE libraries and stores them in a
specified directory
getGEOSAGE(organism = "human", targetDir = "", quiet = TRUE, url = "http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?") getFileNames(organism, url) getSampleId(url)
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 |
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.
getFileNames |
Returns a vector of GPL numbers |
getSampleId |
Returns a vector of platform sample ids |
J. Zhang
http://www.ncbi.nlm.nih.gov/geo/query/
# 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)