stereoAlign.metrics.kbet¶
- stereoAlign.metrics.kbet(data: AnnData, key: str = 'batch', use_rep: str = 'X_umap', alpha: float = 0.05, n_neighbors: int = 30)¶
K-nearest neighbors Batch Effects Test (K-BET)
Calculate the K-nearest neighbors Batch Effects Test (K-BET) metric of the data regarding a specific sample attribute and embedding. The K-BET metric measures if cells from different samples mix well in their local neighborhood.
Parameters¶
- data:
AnnData Data matrix with rows for cells and columns for genes.
- key:
str The sample attribute to be consider. Must exist in
data.obs.- use_rep:
str The embedding representation to be used. The key must be exist in
data.obsm. By default, use UMAP coordinates.- n_neighbors:
int Number of nearest neighbors.
- alpha:
float Threshold. A cell is accepted is its K-BET p-value is greater than or equal to
alpha
Returns¶
- stat_mean:
float Mean K-BET chi-square statistic over all cells.
- pvalue_mean:
float Mean K-BET p-value over all cells.
- accept_rate:
float K-BET acceptance rate of the sample.
- data: