CellScope.fm.FindMarker

CellScope.fm. FindMarker (fea : np.ndarray | csr_matrix, cluster1 : np.ndarray, cluster2 : np.ndarray, selected_number : int = 5, selected_method : str = ‘diff pct’)

The FindMarker function identifies marker genes that differentiate two clusters. It supports various selection methods, such as ‘diff pct’, ‘diff mean’, ‘FC’ (Fold Change), ‘Wilcoxon’ [GE65], and ‘t-test’ [KT15], and returns the top specified number of marker genes.

Parameters

• fea (np.ndarray | csr_matrix):

  The feature matrix of shape (n_cell, n_gene), where rows correspond to cells and columns to genes.

• cluster1 (np.ndarray):

  Indices of cells belonging to the first cluster.

• cluster2 (np.ndarray):

  Indices of cells belonging to the second cluster.

• selected_number (int, optional, default=5):

  Number of top markers to select.

• selected_method (str, optional, default=’diff pct’):

  The method for selecting markers. Options include ‘diff pct’, ‘diff mean’, ‘FC’, ‘Wilcoxon’, and ‘t-test’.

Return

• marker_indices (ndarray):

  Indices of the selected marker genes.

• marker_values (ndarray):

  Corresponding values of the selected markers based on the chosen method.