Ejemplo n.º 1
0
def test_estimate_fdr_digitize_works():
    fdr = FDR(job_id=0, decoy_sample_size=1, target_adducts=['+H'], db=None)
    fdr.fdr_levels = [0.4, 0.8]
    fdr.td_df = pd.DataFrame([['C1', '+H', '+Cu'],
                              ['C2', '+H', '+Ag'],
                              ['C3', '+H', '+Cl'],
                              ['C4', '+H', '+Co']],
                             columns=['sf', 'ta', 'da'])

    msm_df = pd.DataFrame([['C1', '+H', 1.0],
                          ['C2', '+H', 0.75],
                          ['C3', '+H', 0.5],
                          ['C4', '+H', 0.25],
                          ['C1', '+Cu', 0.75],
                          ['C2', '+Ag', 0.3],
                          ['C3', '+Cl', 0.25],
                          ['C4', '+Co', 0.1]],
                          columns=['sf', 'adduct', 'msm']).set_index(['sf', 'adduct']).sort_index()
    exp_sf_df = pd.DataFrame([['C1', '+H', 0.4],
                              ['C2', '+H', 0.4],
                              ['C3', '+H', 0.4],
                              ['C4', '+H', 0.8]],
                             columns=['sf', 'adduct', 'fdr']).set_index(['sf', 'adduct'])

    assert_frame_equal(fdr.estimate_fdr(msm_df), exp_sf_df)
Ejemplo n.º 2
0
def test_estimate_fdr_digitize_works():
    fdr = FDR(job_id=0, decoy_sample_size=1, target_adducts=['+H'], db=None)
    fdr.fdr_levels = [0.4, 0.8]
    fdr.td_df = pd.DataFrame([['C1', '+H', '+Cu'],
                              ['C2', '+H', '+Ag'],
                              ['C3', '+H', '+Cl'],
                              ['C4', '+H', '+Co']],
                             columns=['sf', 'ta', 'da'])

    msm_df = pd.DataFrame([['C1', '+H', 1.0],
                          ['C2', '+H', 0.75],
                          ['C3', '+H', 0.5],
                          ['C4', '+H', 0.25],
                          ['C1', '+Cu', 0.75],
                          ['C2', '+Ag', 0.3],
                          ['C3', '+Cl', 0.25],
                          ['C4', '+Co', 0.1]],
                          columns=['sf', 'adduct', 'msm']).set_index(['sf', 'adduct']).sort_index()
    exp_sf_df = pd.DataFrame([['C1', '+H', 0.4],
                              ['C2', '+H', 0.4],
                              ['C3', '+H', 0.4],
                              ['C4', '+H', 0.8]],
                             columns=['sf', 'adduct', 'fdr']).set_index(['sf', 'adduct'])

    assert_frame_equal(fdr.estimate_fdr(msm_df), exp_sf_df)
Ejemplo n.º 3
0
def test_estimate_fdr_returns_correct_df():
    fdr = FDR(job_id=0, decoy_sample_size=2, target_adducts=['+H'], db=None)
    fdr.fdr_levels = [0.2, 0.8]
    fdr.td_df = pd.DataFrame([['H2O', '+H', '+Cu'], ['H2O', '+H', '+Co'],
                              ['C2H2', '+H', '+Ag'], ['C2H2', '+H', '+Ar']],
                             columns=['sf', 'ta', 'da'])

    msm_df = pd.DataFrame(
        [['H2O', '+H', 0.85], ['C2H2', '+H', 0.5], ['H2O', '+Cu', 0.5],
         ['H2O', '+Co', 0.5], ['C2H2', '+Ag', 0.75], ['C2H2', '+Ar', 0.0]],
        columns=['sf', 'adduct', 'msm']).set_index(['sf',
                                                    'adduct']).sort_index()
    exp_sf_df = pd.DataFrame([['H2O', '+H', 0.2], ['C2H2', '+H', 0.8]],
                             columns=['sf', 'adduct',
                                      'fdr']).set_index(['sf', 'adduct'])

    assert_frame_equal(fdr.estimate_fdr(msm_df), exp_sf_df)
Ejemplo n.º 4
0
def test_estimate_fdr_digitize_works():
    fdr = FDR(0, 0, 1, ['+H'], None)
    fdr.fdr_levels = [0.4, 0.8]
    fdr.td_df = pd.DataFrame([[1, '+H', '+Cu'], [2, '+H', '+Ag'],
                              [3, '+H', '+Cl'], [4, '+H', '+Co']],
                             columns=['sf_id', 'ta', 'da'])

    msm_df = pd.DataFrame(
        [[1, '+H', 1.0], [2, '+H', 0.75], [3, '+H', 0.5], [4, '+H', 0.25],
         [1, '+Cu', 0.75], [2, '+Ag', 0.3], [3, '+Cl', 0.25], [4, '+Co', 0.1]],
        columns=['sf_id', 'adduct', 'msm']).set_index(['sf_id',
                                                       'adduct']).sort_index()
    exp_sf_df = pd.DataFrame(
        [[1, '+H', 0.4], [2, '+H', 0.4], [3, '+H', 0.4], [4, '+H', 0.8]],
        columns=['sf_id', 'adduct', 'fdr']).set_index(['sf_id', 'adduct'])

    assert_frame_equal(fdr.estimate_fdr(msm_df), exp_sf_df)
Ejemplo n.º 5
0
def test_estimate_fdr_returns_correct_df():
    fdr = FDR(0, 0, 2, ['+H'], None)
    fdr.fdr_levels = [0.2, 0.8]
    fdr.td_df = pd.DataFrame([[1, '+H', '+Cu'], [1, '+H', '+Co'],
                              [2, '+H', '+Ag'], [2, '+H', '+Ar']],
                             columns=['sf_id', 'ta', 'da'])

    msm_df = pd.DataFrame([[1, '+H', 0.85], [2, '+H', 0.5], [1, '+Cu', 0.5],
                           [1, '+Co', 0.5], [2, '+Ag', 0.75], [2, '+Ar', 0.0]],
                          columns=['sf_id', 'adduct',
                                   'msm']).set_index(['sf_id',
                                                      'adduct']).sort_index()
    exp_sf_df = pd.DataFrame([[1, '+H', 0.2], [2, '+H', 0.8]],
                             columns=['sf_id', 'adduct',
                                      'fdr']).set_index(['sf_id', 'adduct'])

    assert_frame_equal(fdr.estimate_fdr(msm_df), exp_sf_df)
Ejemplo n.º 6
0
def test_estimate_fdr_returns_correct_df():
    fdr = FDR(job_id=0, decoy_sample_size=2, target_adducts=['+H'], db=None)
    fdr.fdr_levels = [0.2, 0.8]
    fdr.td_df = pd.DataFrame([['H2O', '+H', '+Cu'],
                              ['H2O', '+H', '+Co'],
                              ['C2H2', '+H', '+Ag'],
                              ['C2H2', '+H', '+Ar']],
                             columns=['sf', 'ta', 'da'])

    msm_df = pd.DataFrame([['H2O', '+H', 0.85],
                          ['C2H2', '+H', 0.5],
                          ['H2O', '+Cu', 0.5],
                          ['H2O', '+Co', 0.5],
                          ['C2H2', '+Ag', 0.75],
                          ['C2H2', '+Ar', 0.0]],
                          columns=['sf', 'adduct', 'msm']).set_index(['sf', 'adduct']).sort_index()
    exp_sf_df = pd.DataFrame([['H2O', '+H', 0.2], ['C2H2', '+H', 0.8]],
                             columns=['sf', 'adduct', 'fdr']).set_index(['sf', 'adduct'])

    assert_frame_equal(fdr.estimate_fdr(msm_df), exp_sf_df)