rnalysis.enrichment.FeatureSet.biotypes_from_ref_table

FeatureSet.biotypes_from_ref_table(ref: str | Path | Literal['predefined'] = 'predefined')

Returns a DataFrame describing the biotypes in the gene set and their count.

Parameters:

ref (str or pathlib.Path (default='predefined')) – Path of the reference file used to determine biotype. Default is the path predefined in the settings file.

Examples:

>>> from rnalysis import enrichment, filtering
>>> d = filtering.Filter("tests/test_files/test_deseq.csv")
>>> en = enrichment.FeatureSet(d)
>>> en.biotypes(ref='tests/biotype_ref_table_for_tests.csv')
                gene
biotype
protein_coding    26
pseudogene         1
unknown            1