greatpy.tl.set_bonferroni

greatpy.tl.set_bonferroni(enrichment_df, alpha=0.05)

Create new columns in the dataframe with the Bonferroni correction

Parameters:

enrichment_df : pd.DataFrame

Dataframe with the enrichment computed by enrichment function

alpha : float

alpha value for the Bonferroni correction

Default is 0.05

Returns:

dataframe new columns with the Bonferroni correction for each p-value

Return type:

pd.DataFrame

Examples

>>> test,regdom,size,ann = loader(
    "../data/tests/test_data/input/03_srf_hg19.bed",
    "../data/human/hg19/regulatory_domain.bed",
    "../data/human/hg19/chr_size.bed",
    "../data/human/ontologies.csv"
    )
>>> enrichment = great.tl.enrichment(
    "../data/tests/test_data/input/03_srf_hg19.bed",
    "../data/human/hg19/regulatory_domain.bed",
    "../data/human/hg19/chr_size.bed",
    "../data/human/ontologies.csv",
    binom=True,
    hypergeom=True
    )
>>> bonferroni = set_bonferroni(enrichment,alpha=0.05)
>>> bonferroni.head()
...    |            | go_term                                                          |   binom_p_value |   hypergeom_p_value |   binom_bonferroni |   hypergeom_bonferroni |
...    |:-----------|:-----------------------------------------------------------------|----------------:|--------------------:|-------------------:|-----------------------:|
...    | GO:0045887 | positive regulation of synaptic growth at neuromuscular junction |     5.17744e-13 |          0.0029275  |        3.0754e-10  |                      1 |
...    | GO:0044721 | protein import into peroxisome matrix, substrate release         |     4.83812e-10 |          0.0029275  |        2.87384e-07 |                      1 |
...    | GO:0036250 | peroxisome transport along microtubule                           |     4.83812e-10 |          0.0029275  |        2.87384e-07 |                      1 |
...    | GO:0016561 | protein import into peroxisome matrix, translocation             |     6.31131e-10 |          0.00584656 |        3.74892e-07 |                      1 |
...    | GO:0047485 | protein N-terminus binding                                       |     1.2945e-09  |          0.0050377  |        7.68931e-07 |                      1 |