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 : anndata.AnnData 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.