mira.utils.fetch_factor_hits#
- mira.utils.fetch_factor_hits(atac_adata, factor_type='motifs', mask_factors=False)#
Returns AnnData object of transcription factor binding annotations.
- Parameters
- atac_adataanndata.AnnData
AnnData object of ATAC features
- mask_factorsboolean, default = False
Whether to subset the list of TFs returned to those flagged by “subset_factors”.
- factor_type{‘motifs’,’chip’}, default=’motifs’
Which factor type to filter.
- Returns
- anndata.AnnData:
- .obspd.DataFrame
TF annotation metadata.
- .varpd.DataFrame
Peak metadata taken from atac_adata.
- Xscipy.sparsematrix
TF binding predictions. For motifs, values show MOODS3 “Match Score”, with higher values indicating a better match between a peak sequence and motif PWM. For ChIP-seq samples, values are binary, with 1 indicating overlap with a peak in a Cistrome ChIP-seq sample.