Description Usage Arguments Details Author(s) See Also Examples
View source: R/loadDataToCompendium.R
Load the data from SOFT files corresponding to the
specified GSE and GPL(s) into the tables of the MySQL
compendium database
1 | loadDataToCompendium(con, GSEid, GPLid = "", datadir = getwd())
|
con |
|
GSEid |
character string specifying the GSE ID to be loaded into the compendium database |
GPLid |
character vector specifying the GPL ID(s). The default value is
|
datadir |
directory where the BigMac directory used for storing the SOFT files
downloaded from GEO has been created (see
|
The SOFT files downloaded from GEO using the function
downloadGEOdata
are parsed and loaded into the
compendium database. This function can be called once all the
SOFT files corresponding to the specified GSEid
have been downloaded
to the BigMac
directory (see downloadGEOdata
).
The BigMac
directory should be a subdirectory of the directory specified by the
user via the argument datadir
. The GPLid
argument provides
the option to only load the data for a specific platform.
Umesh K. Nandal
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## Not run:
conn <- connectDatabase(user="usrname",password="passwd",dbname="compendium")
downloadGEOdata("GSE1657")
# GSE1657 has GPL96 and GPL97 platform data. Load only GPL96 data
loadDataToCompendium(conn,"GSE1657","GPL96")
# Load both GPL96 and GPL97 as a character vector
loadDataToCompendium(conn,"GSE1657",c("GPL96","GPL97"))
# Both platforms can also be loaded using the default value for GPLid
# Load multiple GSEs to the compendium
for (i in c("GSE4251","GSE6495","GSE12597","GSE1657")){
loadDataToCompendium(con=conn,GSEid=i)
}
## End(Not run)
|
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