mieaa.API.run_gsea¶
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API.run_gsea(test_set: Union[str, Iterable[T_co], IO], categories: Iterable[T_co], mirna_type: str, species: str, **kwargs)¶ Start miRNA Set Enrichment Analysis
Parameters: - test_set (str, iterable or file-like) – set of miRNAs/precursors we want to test
- categories (str, iterable or file-like) – Categories we want to run analysis on
- mirna_type (str) –
- precursor - Precursor to a mature miRNA, e.g. hsa-mir-550b-1
- mirna - Mature miRNA, e.g. hsa-miR-199a-5p
- species (str) –
- hsa - Homo sapiens
- mmu - Mus musculus
- rno - Rattus norvegicus
- ath - Arabidopsis thaliana
- bta - Bos taurus
- cel - Caenorhabditis elegans
- dme - Drosophila melanogaster
- dre - Danio rerio
- gga - Gallus gallus
- ssc - Sus scrofa
- **kwargs –
- p_value_adjustment (str, default=’fdr’)
- none - No adjustment
- fdr - FDR (Benjamini-Hochberg) adjustment
- bonferroni - Bonferroni adjustment
- BY - Benjamini-Yekutieli adjustment
- hochberg - Hochberg adjustment
- holm - Holm adjustment
- hommel - Hommel adjustment
- independent_p_adjust (bool, default=True)
- True - Adjust p-values for each category independently
- False - Adjust p-values for all categories collectively
- significance_level (float, default=0.05)
- Filter out p-values above significance level
- threshold_level (int, default=2)
- Filter out subcategories that contain less than this many miRNAs
Returns: Response
Return type: requests.Response