def get_tf_associations(self, test):
# test = {not dissociated,associated}
tf_set = set()
# this is the set in which all Term - Function pairs will be contained
# that cannot be dissociated (i.e, for which we do not know for sure that
# they are not associated) - done with Fisher Exact tests
for onto in set(self.ontological):
if onto not in ['body','thing']: continue
d_onto = self.data[self.ontological == onto]
for li in range(30):
terms = set([w for dd in d_onto for w in dd[li]])
for term in terms:
for annot in set(self.annotation):
valid = False
if annot == 'UF': continue
d_onto_annot = self.data[(self.ontological == onto) * (self.annotation == annot)]
aa = len([t for t in d_onto_annot if term in t[li]]) # + term + function
ab = len(d_onto_annot) - aa # - term + function
ba = len([t for t in d_onto if term in t[li]]) - aa # + term - function
bb = len(d_onto) - (aa + ab + ba) # - term - function
if test == 'not dissociated' and fisher_exact([[aa,ab],[ba,bb]],'less')[1] > .05:
valid = True
tf_set.add((li,term,annot))
if test == 'associated' and fisher_exact([[aa,ab],[ba,bb]],'greater')[1] < .05:
valid = True
tf_set.add((li,term,annot))
# if aa > 0: print('%s,%d,%s,%s,%r,%d,%d,%d' % (onto,li,term,annot,valid,aa,ba,ab))
return tf_set
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