getGEOMetadata {Onassis} | R Documentation

## `getGEOMetadata`

### 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')
    }

[Package Onassis version 1.12.0 Index]