Changeset 1849:bd2ced9dddb8 in orange-bioinformatics


Ignore:
Timestamp:
10/01/13 16:22:16 (7 months ago)
Author:
markotoplak
Branch:
default
Message:

Widget rename: Gene selection -> Differential expression

Location:
_bioinformatics
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • _bioinformatics/obiGeneSetSig.py

    r1803 r1849  
    7474 
    7575        #build a new domain 
     76        print "WHOLE" 
    7677        newfeatures = self.build_features(data, gene_sets) 
    7778        newdomain = Orange.data.Domain(newfeatures, data.domain.class_var) 
     
    9091            data_cv = [ [] for _ in range(len(data)) ] 
    9192            for f in set(cvi): 
     93                print "FOLD", f 
    9294                learn = data.select(cvi, f, negate=True) 
    9395                test = data.select(cvi, f) 
     
    98100                    zip(trans_test, [ i for i,n in enumerate(cvi) if n == f ]): 
    99101                    data_cv[pos] = ex.native(0) 
     102            print data_cv[0] 
    100103            return Orange.data.Table(newdomain, data_cv) 
    101104 
     
    614617            break 
    615618         
    616     return sortedinds[:bg] #FIXED - one too many was taken 
     619    return sortedinds[:bg] 
    617620 
    618621class CORGs(ParametrizedTransformation): 
     
    636639        ind_names = dict( (a,b) for b,a in name_ind.items() ) 
    637640        selected_genes = sorted(set([to_geneset[ind_names[i]] for i in indices])) 
    638              
     641     
    639642        def t(ex, w, corg=selected_genes): #copy od the data 
    640643            nm2, name_ind2, genes2 = self._match_instance(ex, corg, None) 
     
    907910    ass = LLR(data, matcher=matcher, gene_sets=gsets, class_values=choosen_cv, min_part=0.0, normalize=True) 
    908911    #ass = LLR_slow(data, matcher=matcher, gene_sets=gsets, class_values=choosen_cv, min_part=0.0) 
     912    ass = CORGs(data, matcher=matcher, gene_sets=gsets, class_values=choosen_cv, min_part=0.0, cv=True) 
    909913    ar = to_old_dic(ass.domain, data[:5]) 
    910914    pp2(ar) 
  • _bioinformatics/widgets/OWFeatureSelection.py

    r1726 r1849  
    11""" 
    2 <name>Gene Selection</name> 
     2<name>Differential expression</name> 
    33<description>Gene differential expression scoring and selection.</description> 
    44<priority>1010</priority> 
     
    322322                not (self.attribute_targets or self.class_targets): 
    323323            # If both attr. labels and classes are missing, show an error 
    324             self.error(1, "Cannot compute gene scores! Gene Selection widget " 
     324            self.error(1, "Cannot compute gene scores! Differential expression widget " 
    325325                          "requires a data-set with a discrete class variable " 
    326326                          "or attribute labels!") 
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