def test_0(regtest):
p_values = np.linspace(0.0, 1., 50)
p_values = np.append(p_values, np.linspace(1.0 - 0.0001, 1.0, 50))
df = get_error_table_from_pvalues_new(p_values, use_pfdr=False).df
print("without correction", file=regtest)
print(df.head(), file=regtest)
print(df.tail(), file=regtest)
df = get_error_table_from_pvalues_new(p_values, use_pfdr=True).df
# we should see non nan here for FDR:
print("with correction", file=regtest)
print(df.head(), file=regtest)
print(df.tail(), file=regtest)
def test_0(regtest):
p_values = np.linspace(0.0, 1., 50)
p_values = np.append(p_values, np.linspace(1.0 - 0.0001, 1.0, 50))
df = get_error_table_from_pvalues_new(p_values, use_pfdr=False).df
print("without correction", file=regtest)
print(df.head(), file=regtest)
print(df.tail(), file=regtest)
df = get_error_table_from_pvalues_new(p_values, use_pfdr=True).df
# we should see non nan here for FDR:
print("with correction", file=regtest)
print(df.head(), file=regtest)
print(df.tail(), file=regtest)
num_pos = m - num_negs
pp = num_pos / float(m)
qvalues = np.ones(m)
qvalues[0] = pFDR[0]
for i in range(m-1):
qvalues[i+1] = min(qvalues[i], pFDR[i+1])
sens = ((1.0 - qvalues) * num_pos) / num_alt
sens[sens > 1.0] = 1.0
df = pd.DataFrame(dict(
pvalue=pvalues,
qvalue=qvalues,
FDR=pFDR,
percentile_positive=pp,
sens=sens
))
df["svalue"] = df.sens[::-1].cummax()[::-1]
return df, num_null, m
errstat = get_error_table_from_pvalues_new(p_values, 0.4, True)
fdr_pyprophet = errstat.df["FDR"]
df, __, __ = calc(p_values, 0.4)
fdr_storey = df["FDR"]
fdrs = pd.DataFrame(dict(fdr_pp=fdr_pyprophet, fdr_storey=fdr_storey))
print(fdrs[:34])
print(fdrs[:])
num_pos = m - num_negs
pp = num_pos / float(m)
qvalues = np.ones(m)
qvalues[0] = pFDR[0]
for i in range(m - 1):
qvalues[i + 1] = min(qvalues[i], pFDR[i + 1])
sens = ((1.0 - qvalues) * num_pos) / num_alt
sens[sens > 1.0] = 1.0
df = pd.DataFrame(
dict(pvalue=pvalues,
qvalue=qvalues,
FDR=pFDR,
percentile_positive=pp,
sens=sens))
df["svalue"] = df.sens[::-1].cummax()[::-1]
return df, num_null, m
errstat = get_error_table_from_pvalues_new(p_values, 0.4, True)
fdr_pyprophet = errstat.df["FDR"]
df, __, __ = calc(p_values, 0.4)
fdr_storey = df["FDR"]
fdrs = pd.DataFrame(dict(fdr_pp=fdr_pyprophet, fdr_storey=fdr_storey))
print(fdrs[:34])
print(fdrs[:])
