Changeset 1936:847a781b8798 in orange-bioinformatics


Ignore:
Timestamp:
12/13/13 14:40:06 (4 months ago)
Author:
markotoplak
Branch:
default
Message:

obiGEO documentation: partial conversion to rst.

Files:
3 edited

Legend:

Unmodified
Added
Removed
  • docs/rst/index.rst

    r1934 r1936  
    3030   reference/genesets.rst 
    3131   reference/prob.rst 
     32   reference/geo.rst 
    3233 
    3334Installation 
  • docs/rst/reference/genesets.rst

    r1933 r1936  
    99 
    1010:mod:`obiGeneSets` can load gene sets distributed with Orange (through ServerFiles)  
    11 and also in GMT file format. 
     11and also in `GMT file format <http://www.molmine.com/magma/fileformats.html>`_. 
    1212 
    1313Load gene sets from KEGG and GO for mouse:: 
  • orangecontrib/bio/obiGEO.py

    r1873 r1936  
    4040 
    4141class GDSInfo: 
     42 
     43    """ 
     44    Retreive the infomation about `GEO DataSets 
     45    <http://www.ncbi.nlm.nih.gov/sites/GDSbrowser>`_.  The class accesses 
     46    the Orange server file that either resides on the local computer or 
     47    is automatically retreived from Orange server. Notice that the call 
     48    of this class does not access any NCBI's servers directly. 
     49 
     50    Constructor returning the object with GEO DataSets information. If 
     51    :obj:`force_update` is True, the constructor will download GEO DataSets 
     52    information file (gds_info.pickled) from Orange server, otherwise, 
     53    it will first check if the local copy exists. 
     54 
     55    An instance behaves like a dictionary: the keys are GEO DataSets 
     56    IDs, and the dictionary values for is a dictionary providing various 
     57    information about the particular data set. 
     58    """ 
     59 
    4260    def __init__(self, force_update=False): 
    4361        path = orngServerFiles.localpath(DOMAIN, GDS_INFO_FILENAME) 
     
    6583 
    6684class GDS(): 
    67     """GEO DataSet class: read GEO datasets and convert them to ExampleTable.""" 
     85    """  
     86    GDS is a class that 
     87    provides methods for retreival of a specific GEO DataSet. The data 
     88    is provided as a :obj:`Orange.data.Table`. 
     89 
     90    Constructor returning the object to be used to retreive 
     91    GEO DataSet table (samples and gene expressions). Checks 
     92    a local cache directory if the particular data file is 
     93    loaded locally, else it downloads it from `NCBI's GEO FTP site 
     94    <ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/>`_.  The compressed 
     95    data file resides in the cache directory after the call of the 
     96    constructor (call to ``orngServerFiles.localpath("GEO")`` reveals 
     97    the path of this directory). 
     98 
     99    :param gdsname: an NCBI's ID for the data set in the form "GDSn" 
     100      where "n" is a GDS ID number. 
     101 
     102    :param force_download: force the download. 
     103 
     104    """ 
     105 
    68106    def __init__(self, gdsname, verbose=False, force_download=False): 
    69107        self.gdsname = gdsname 
     
    264302                 sample_type=None, missing_class_value=None, 
    265303                 transpose=False, remove_unknown=None): 
    266         """Load GDS data and returns a corresponding orange data set, 
    267         spot<->gene mappings and subset info.""" 
     304        """ 
     305        Returns the data from GEO DataSet in 
     306        Orange format.  
     307 
     308        :param report_genes: Micorarray spots reported in the GEO data set can 
     309          either be merged according to their gene id's 
     310          (if True) or can be left as spots.  
     311 
     312        :param transpose: The data 
     313          table can have spots/genes in rows and samples in columns 
     314          (False, default) or samples in rows and  spots/genes in columns 
     315          (True).  
     316 
     317        :param sample_type: the type of annotation, or (if :obj:`transpose` is True) 
     318          the type of class labels to be included in the data set. 
     319          The entire annotation of samples will 
     320          be included either in the class value or in 
     321          the ``.attributes`` field of each data set 
     322          attributes.  
     323 
     324        :param remove_unknown: Remove spots with sample profiles that 
     325          include unknown values. They are removed if the proportion 
     326          of samples with unknown values is above the threshold set by 
     327          ``remove_unknown``. If None, nothing is removed. 
     328        """ 
    268329        if self.verbose: print "Reading data ..." 
    269330#        if not self.gdsdata: 
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