![[Experimental]](figures/lifecycle-experimental.svg)
The function takes in a kNN matrix and a batch vector indicating which
cell belongs to which batch. For the neighbourhood of each cell, a
chi-square test checks whether the batch proportions differ from the
overall batch proportions (with Yates' correction for two batches). Good
mixing means few cells with significant differences; bad mixing means
many.
Usage
rs_kbet(knn_mat, batch_vector, verbose)
Arguments
- knn_mat
Integer matrix. The rows represent the cells and the
columns the neighbour indices (0-indexed!).
- batch_vector
Integer vector. The batch per cell. The codes need
not be 0-based or contiguous.
- verbose
Boolean. Controls verbosity of the function.
Value
A list with the following items
pval - Per-cell p-values from the chi-square test.
chi_square_stats - Per-cell chi-square statistics.
mean_chi_square - The mean chi-square value.
median_chi_square - The median chi-square value.
