Rna.get_markers#
missionbio.mosaic.rna.Rna.get_markers
- Rna.get_markers(layer: str = 'normalized_counts', split_by: str = 'label', method: str = 'welch', top_n_markers: int = 5, min_cluster_size: int = 10) RNAClusterMarkers#
Get the markers for each RNA cluster using DE analysis
- Parameters:
- method: str
The DE method to use. “welch” or “wilcoxon” currently implemented
- top_n_markers: int
How many top markers from each grouping (RNA label) to include in markers table
- min_cluster_size: int
Minimum # of cells in smallest group. Will raise ValueError “Not enough cells in either group.” if the smallest group has fewer than min_cells cells
- layer: str
The RNA data layer to use
- split_by: str
RNA row attribute to call markers on
- Returns:
- missionbio.mosaic.algorithms.rna.cluster_markers.RNAClusterMarkers