greatpy.tl.enrichment_multiple

greatpy.tl.enrichment_multiple(tests, regdom_file, chr_size_file, annotation_file, annpath='../../annotation/', binom=True, hypergeom=True)

Compute the enrichment of GO term for multiple tests sets using bindome or a list of file path.

Parameters:

tests : list

List of complete name of data to compute

regdom_file : str or pd.DataFrame

Regulatory domain of all genes in the genome

chr_size_file : str or pd.DataFrame

Table with the size of each chromosome

annotation_file : str or pd.DataFrame

Table with the annotation of each gene in the genome

annpath : str or None, optional

Path to the annotation files used for bindome computation.

If None, the function doesn’t use bindome.

Default is "../../annotation/"

binom : bool

If True, the binomial test is used.

Default is True

hypergeom : bool

If True, the hypergeometric test is used.

Default is True

Returns:

List of dataframe with the enrichment of each test

Return type:

dict

Examples

>>> tests = ["MAX:K-562,WA01,HeLa-S3", "BACH1:A-549,GM12878"]
>>> enrichment = enrichment_multiple(
        tests = tests,
        regdom_file="../data/human/hg38/regulatory_domain.bed",
        chr_size_file="../data/human/hg38/chr_size.bed",
        annotation_file="../data/human/ontologies.csv",
        binom=True,
        hypergeom=True,
    )
>>> enrichment
...    {'MAX': pd.DataFrame,
...    'BACH1': pd.DataFrame}