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obiGEO documentation: partial commit.

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docs/rst/reference/geo.rst

+.. py:currentmodule:: Orange.bio.obiGEO
+
+.. index:: NCBI
+.. index:: GEO
+.. index:: Gene Expression Omnibus
+.. index:: microarray data sets
+
+**************************************************************
+An interface to NCBI's Gene Expression Omnibus (:mod:`obiGEO`)
+**************************************************************
+
+:obj:`obiGEO` provides an interface to `NCBI
+<http://www.ncbi.nlm.nih.gov/>`_'s `Gene Expression Omnibus
+<http://www.ncbi.nlm.nih.gov/geo/>`_ repository. Currently, it only
+supports `GEO DataSets <http://www.ncbi.nlm.nih.gov/sites/GDSbrowser>`_
+information querying and retrieval.
+
+The following illustrates how :obj:`GDS.getdata` is used to
+construct a data set with genes in rows and samples in
+columns. Notice that the annotation about each sample is retained
+in ``.attributes``.
+
+::
+
+    >>> from Orange.bio import obiGEO
+    >>> gds = obiGEO.GDS("GDS1676")
+    >>> data = gds.getdata()
+    >>> len(data)
+    667
+    >>> data[0]
+    [?, ?, -0.803, 0.128, 0.110, -2.000, -1.000, -0.358], {"gene":'EXO1'}
+    >>> data.domain.attributes[0]
+    FloatVariable 'GSM63816'
+    >>> data.domain.attributes[0].attributes
+    Out[191]: {'dose': '20 U/ml IL-2', 'infection': 'acute ', 'time': '1 d'}
+
+GDS
+===
+
+.. autoclass:: GDSInfo
+   :members:
+
+::
+
+    >>> import obiGEO
+    >>> info = obiGEO.GDSInfo()
+    >>> info.keys()[:5]
+    >>> ['GDS2526', 'GDS2524', 'GDS2525', 'GDS2522', 'GDS1618']
+    >>> info['GDS2526']['title']
+    'c-MYC depletion effect on carcinoma cell lines'
+    >>> info['GDS2526']['platform_organism']
+    'Homo sapiens'
+
+.. autoclass:: GDS
+   :members:
+
+
+Examples
+==================
+
+Genes can have multiple aliases. When we combine data from different
+sources, for example expression data with GO gene sets, we have to
+match gene aliases representing the same genes. All implemented matching
+methods are based on sets of gene aliases for one gene.
+
+.. autoclass:: Matcher
+   :members:
+
+This modules provides the following gene matchers:
+
+.. autoclass:: MatcherAliasesKEGG
+
+.. autoclass:: MatcherAliasesGO
+
+.. autoclass:: MatcherAliasesDictyBase
+
+.. autoclass:: MatcherAliasesNCBI
+
+.. autoclass:: MatcherAliasesEnsembl
+
+.. autoclass:: MatcherDirect
+
+Gene name matchers can applied in sequence (until the first match) or combined (overlapping sets of gene aliases of multiple gene matchers are combined) with the :obj:`matcher` function.
+
+.. autofunction:: matcher
+
+The following example tries to match input genes onto KEGG gene aliases (:download:`genematch2.py <code/genematch2.py>`).
+
+.. literalinclude:: code/genematch2.py
+
+Results show that GO aliases can not match onto KEGG gene IDs. For the last gene only joined GO and KEGG aliases produce a match::
+
+        gene         KEGG           GO      KEGG+GO
+        cct7    hsa:10574         None    hsa:10574
+        pls1     hsa:5357         None     hsa:5357
+        gdi1     hsa:2664         None     hsa:2664
+       nfkb2     hsa:4791         None     hsa:4791
+      a2a299         None         None     hsa:7052
+
+
+The following example finds KEGG pathways with given genes (:download:`genematch_path.py <code/genematch_path.py>`).
+
+.. literalinclude:: code/genematch_path.py
+
+Output::
+
+    Fndc4 is in
+      /
+    Itgb8 is in
+      PI3K-Akt signaling pathway
+      Focal adhesion
+      ECM-receptor interaction
+      Cell adhesion molecules (CAMs)
+      Regulation of actin cytoskeleton
+      Hypertrophic cardiomyopathy (HCM)
+      Arrhythmogenic right ventricular cardiomyopathy (ARVC)
+      Dilated cardiomyopathy
+    Cdc34 is in
+      Ubiquitin mediated proteolysis
+      Herpes simplex infection
+    Olfr1403 is in
+      Olfactory transduction
+
+