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getter/display methods for Bgee and topAnatData classes #19

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julien-roux opened this issue Jun 20, 2017 · 0 comments
Open

getter/display methods for Bgee and topAnatData classes #19

julien-roux opened this issue Jun 20, 2017 · 0 comments

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@julien-roux
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It is a good practice to provide to the users some getters to access/format the internal slots of the objects

  • It would be nice to implement "classical" getters, such as organism() for Bgee class objects
  • It would be nice to define a "show" method for Bgee class objects to display the object in a user friendly way
  • Currently the topAnatData objects are shown using the show method of the topGOdata class (that it inherits) and is not so appropriate. For example:

------------------------- topGOdata object -------------------------

 Description:
   -  topAnatData class object, ready for anatomical ontology enrichment test 

 Ontology:
   -  UBERON ontology describing animal anatomical structures 

 100 available genes (all genes from the array):
   - symbol:  ENSMUSG00000064370 ENSMUSG00000064368 ENSMUSG00000064367 ENSMUSG00000064363 ENSMUSG00000065947  ...
   - 10  significant genes. 

 99 feasible genes (genes that can be used in the analysis):
   - symbol:  ENSMUSG00000064370 ENSMUSG00000064368 ENSMUSG00000064367 ENSMUSG00000064363 ENSMUSG00000065947  ...
   - 9  significant genes. 

 GO graph (nodes with at least  1  genes):
   - a graph with directed edges
   - number of nodes = 182 
   - number of edges = 278 

------------------------- topGOdata object -------------------------

This method could be overwritten to display topAnatData object in a more relevant manner (without refering to GO for example...). See the topGO show method:

selectMethod("show", "topAnatData")
topGO:::.printTopGOdata
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