getGEOMetadata {Onassis} | R Documentation |
getGEOMetadata
This method retrierves the descriptive fields of the samples in GEO for a given experiment_type, organism or platform.
getGEOMetadata(geo_con, experiment_type = NA, organism = NA, gpl = NA)
geo_con |
connection to the SQLite GEOmetadb databse |
experiment_type |
The type of experiment. Allowed values can be obtained through the function |
organism |
Optional type of organism. Allowed species can be obtained using the function |
gpl |
Optional platform identifier in case a platform based query has to be executed |
A data frame with the queried samples' metadata
if(file.exists('GEOmetadb.sqlite')){ geo_con <- connectToGEODB('GEOmetadb.sqlite') methilation <- getGEOMetadata(geo_con, 'Methylation profiling by high throughput sequencing', 'Homo sapiens') expression <- getGEOMetadata(geo_con, 'Expression profiling by array', 'Homo sapiens', 'GPL570') }else{ print('You need to download GEOmetadb.sqlite to run this example') }