geoquery: querying the GEO database

Example

import bioc.geoquery

gds = bioc.geoquery.__rpackage__.getGEO("GDS12")

>>> tuple(gds.meta.rx2("description"))
('Examination of two functionally distinct human bone marrow stromal cell lines, HS-27a and HS-5. Four independent RNA samples from each cell line analyzed.',
 'HS-5',
 'HS-27a')

Docstrings

The class inheritance diagram presents the parent-child relationships between the elements.

The module reflects some of the content of the R/Bioconductor package GEOquery. It defines Python-level classes for the R/S4 classes, and gives otherwise access to R-level commands the usual rpy2:robjects way.

In complement to this module, it is recommended to also use ‘rpy2.robjects.packages.importr’ to expose the full content of GEOquery

>>> import bioc.geoquery

Now all methods exposed by the R package are accessible from ‘bio.geoquery.__rpackage__’, with Python classes defined in bioc.geoquery mapping the R classes.

class bioc.geoquery.GDS

GEO ‘datasets’ entity

class bioc.geoquery.GEOData

R ‘virtual’ class (that is an abstract class)

accession

GEO accession number

columns

column descriptions

datatable

data table

meta

meta-data (sample information)

table

table

class bioc.geoquery.GEODataTable

columns

column descriptions

table

table

class bioc.geoquery.GPL

GEO ‘platforms’ entity

class bioc.geoquery.GSM

GEO ‘samples’ entity

bioc.geoquery.geoquery_conversion(robj)