scmags.ScMags.sel_clust_marker¶

ScMags.sel_clust_marker(nof_markers=3, n_cores=- 2, dyn_prog=False)[source]¶

Performs cluster-specific marker selection among filtered genes. It does this in two different ways.

Parameters

nof_markers (Optional[int]) – Number of markers to be selected for each cluster.
n_cores (Optional[int]) – Number of cores to use. (If not given = total number of cores -1)
dyn_prog (bool) – Marker selection status with dynamic programming. If True, the combinational genes are combined and the gene combination with the highest silhouette value is selected.

Examples

>>> import scmags as mg
Li Dataset
>>> li = mg.datasets.li()
Filtering out unnecessary genes
>>> li.filter_genes()
Selection of markers from remaining genes
>>> li.sel_clust_marker()
Get markers
>>> li.get_markers()
Get markers data
>>> li.get_marker_data()