scFates.tl.fit¶
- scFates.tl.fit(adata, features=None, layer=None, n_map=1, n_jobs=1, gamma=1.5, save_raw=True, copy=False)¶
Model feature expression levels as a function of tree positions.
The models are fit using mgcv R package. Note that since adata can currently only keep the same dimensions for each of its layers. While the dataset is subsetted to keep only significant feratures, the unsubsetted dataset is kept in adata.raw (save_raw parameter).
- Parameters
- adata :
AnnData Annotated data matrix.
- layer :
str|NoneOptional[str] (default:None) adata layer to use for the fitting.
- n_map :
int(default:1) number of cell mappings from which to do the test.
- n_jobs :
int(default:1) number of cpu processes used to perform the test.
- gamma :
float(default:1.5) stringency of penalty.
- saveraw
save the unsubsetted anndata to adata.raw
- copy :
bool(default:False) Return a copy instead of writing to adata.
- adata :
- Returns
adata – if copy=True it returns subsetted or else subset (keeping only significant features) and add fields to adata:
- .layers[‘fitted’]
fitted features on the trajectory for all mappings.
- Return type