getGEOMetadata: 'getGEOMetadata'

In eugeniaeueu/Onassis: OnASSIs Ontology Annotation and Semantic SImilarity software

Description

This method retrierves the descriptive fields of the samples in GEO for a given experiment_type, organism or platform.

Usage

getGEOMetadata(geo_con, experiment_type = NA, organism = NA,
  gpl = NA)

Arguments

geo_con	connection to the SQLite GEOmetadb databse
experiment_type	The type of experiment. Allowed values can be obtained through the function experiment_types
organism	Optional type of organism. Allowed species can be obtained using the function organism_types. If no organism is passed as parameter the query will retrieve all the organisms
gpl	Optional platform identifier in case a platform based query has to be executed

Value

A data frame with the queried samples' metadata

Examples

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')
}

eugeniaeueu/Onassis documentation built on March 9, 2020, 8:17 a.m.