mira.utils.subset_factors#
- mira.utils.subset_factors(atac_adata, *, use_factors, factor_type='motifs')#
Subset which transcription factor binding annotations are used in downstream analysis. This function marks annotations if the factor is in the list provided to use_factors, but does not erase out-of-list factors’ information. Thus, a new subset may be applied without re-scanning for motifs.
Important: we do not suggest subsetting to transcription factors that have high or highly dispersed expression in multiomics analyses. Many transcription factors may have potent regulatory effects without showing a great change in expression.
- Parameters
- atac_adataanndata.AnnData
AnnData object of ATAC features
- use_factorsnp.ndarray[str], list[str]
List of transcription factor names to use for downstream analysis.
- factor_type{‘motifs’,’chip’}, default=’motifs’
Which factor type to filter.
- Returns
- anndata.AnnData