Tailored function for finding neighbors in lower dimensional space.

This function adapts the Seurat FindNeighbors function by also checking if 'dims' is larger than dimensions in 'reduction' object. If yes, it takes maximum columns of 'reduction' object.

Usage

find_neighbors(seu, dims, reduction, ...)

Arguments

seu

Seurat object (required).

dims

Vector denoting which dimensions to use as input features, e.g. dims = 1:30

reduction

Reduction object to run UMAP. E.g. can be 'pca' or 'harmony' for integrated data (required).

...

Additional named parameters to Seurat FindNeighbors function.

Value

Seurat object.

Author

C.A.Kapourani C.A.Kapourani@ed.ac.uk