scFates.pp.find_overdispersed¶
- scFates.pp.find_overdispersed(adata, gam_k=5, alpha=0.05, layer='X', plot=False, copy=False)¶
Find overdispersed gene, using pagoda2 strategy.
Code has been translated from pagoda2 R function adjustVariance.
- Parameters
- adata
Annotated data matrix.
- gam_k :
int(default:5) The k used for the generalized additive model.
- alpha :
float(default:0.05) The criterion used to measure statistical significance.
- layer :
str(default:'X') Which layer to use.
- plot :
bool(default:False) Plot selected genes.
- copy :
bool(default:False) Return a copy instead of writing to adata.
- Returns
adata –
if copy=True it returns or else add fields to adata:
- .var[‘res’]
residuals of GAM fit.
- .var[‘lp’]
p-value.
- .var[‘lpa’]
BH adjusted p-value.
- .var[‘qv’]
percentile of qui-squared distribution.
- .var[‘highly_variable’]
feature is over-dispersed.
- Return type