pegasus.markers¶
-
pegasus.
markers
(data, head=None, de_key='de_res', sort_by='auroc,WAD_score', alpha=0.05)[source]¶ - Parameters
data (
anndata.AnnData
) – Annotated data matrix with rows for cells and columns for genes.head (
int
, optional, default:None
) – List only tophead
genes for each cluster. IfNone
, show any DE genes.de_key (
str
, optional, default,de_res
) – Keyword of DE result stored indata.varm
.sort_by (
str
, optional, default:"auroc,WAD_score"
) – Sort the resulting marker dictionary byauroc
andWAD_score
.alpha (
float
, optional, default:0.05
) – q-value threshold for getting valid DE genes. Only those with q-value of any test belowalpha
are significant, and thus considered as DE genes.
- Returns
results – A Python dictionary containing markers in structure
dict[cluster_id]['up' or 'down'][dataframe]
.- Return type
Dict[str, Dict[str, pd.DataFrame]]
Examples
>>> marker_dict = pg.markers(adata)