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cistrome / MIRA

Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.
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What is the best way to decide whether a gene is NITE or LITE regulated? #11

Closed shaistamadad closed 2 years ago

shaistamadad commented 2 years ago

Hi, Is there a set of p-values associated with the NITE scores for genes and cells in your RP model? I am trying to find a quantitative metric to decide whether a set of genes I am interested in are NITE or LITE regulated. I understand from your tutorial that plotting the chromatin differential plots is one way of checking this. 

lite_model.get_logp(expr_adata=rna_sub, atac_adata=atac_data)
nite_model.get_logp(expr_adata=rna_sub, atac_adata=atac_data)
mira.tl.get_NITE_score_genes(rna_sub)
mira.tl.get_NITE_score_cells(rna_sub)
AllenWLynch commented 2 years ago

We do not usually define a hard cut off between LITE and NITE, but the way to decide which way a gene swings is to visualize the distribution of NITE scores across all modeled genes. If a gene you are interested in is on the tail of the distribution, I would consider it more NITE.