def test(self): """Test Benjamini-Hochberg P-value adjustment""" adjps = stats.adjustPValues([0.1,0.2,0.3,0.4], method='FDR') self.assertTrue(round(adjps[0],1)==0.4) self.assertTrue(round(adjps[1],1)==0.4) self.assertTrue(round(adjps[2],1)==0.4) self.assertTrue(round(adjps[3],1)==0.4) adjps = stats.adjustPValues([0.1,0.2,0.003], method='fdr') self.assertTrue(round(adjps[0],2)==0.15) self.assertTrue(round(adjps[1],1)==0.2) self.assertTrue(round(adjps[2],3)==0.009)
def test(self):
"""Test Benjamini-Hochberg P-value adjustment, ordering"""
sp.random.seed(111)
n = 3
#pvals = sp.array(range(n-1,-1,-1))/1.0e5
#ranks = st.rankdata(sp.random.random(len(pvals)))
#pvals = [pvals[x-1] for x in ranks]
pvals = [0.0, 2e-5, 1e-5]
adjps = stats.adjustPValues(pvals, method='FDR')
#print ""
#for i in range(n):
# print "{:1.6E}\t{:1.6E}".format(pvals[i],adjps[i])
for i in range(n):
self.assertTrue(adjps[i] >= pvals[i])
p_value_list.append(pval)
try:
length_dict[length].append(key)
except KeyError:
length_dict[length] = [key]
except KeyError:
print "Erroring...this should not continue"
p_value_dict[key] = 1.0
p_value_list.append(1.0)
continue
if options.adjust:
# Each distribution, based on length, gets its own correction
for length in length_dict.keys():
len_keys = length_dict[length]
p_values = [p_value_dict[lk] for lk in len_keys]
adjusted_p_values = stats.adjustPValues(p_values, method='FDR')
for (i,k) in enumerate(len_keys):
adjusted_p_value_dict[k] = adjusted_p_values[i]
#adjusted_p_value_dict = dict([(k, v) for (k,v) in zip(keys, adjusted_p_values)])
# Write output
n_written = 0
# Tack sequence on the end, for better readability
columns = headers[:]
columns.remove('sequence')
data_outs.write('\t'.join(columns) + "\tp.value\tp.value.adj\tsequence\n")
for key in keys:
flds = data[key]
#entropy = flds['entropy']
#length = flds['length'] # length of the region
pval = p_value_dict[key]
def test(self): """Test Benjamini-Hochberg P-value adjustment, ordering""" pvals = sp.array(range(100,-1,-1))/1.0e5 adjps = stats.adjustPValues(pvals, method='FDR') for i in range(1,10): self.assertTrue(adjps[i]<adjps[i-1])