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_from_ref_table(ref='tests/test_files/biotype_ref_table_for_tests.csv')
Biotype Reference Table used: tests/test_files/biotype_ref_table_for_tests.csv
shape: (3, 2)
┌────────────────┬───────┐
│ biotype        ┆ count │
│ ---            ┆ ---   │
│ str            ┆ u32   │
╞════════════════╪═══════╡
│ protein_coding ┆ 26    │
│ pseudogene     ┆ 1     │
│ unknown        ┆ 1     │
└────────────────┴───────┘