find_neighbors: Tailored function for finding neighbors in lower dimensional...

In andreaskapou/SeuratPipe: Packaging common Seurat analysis tasks

Tailored function for finding neighbors in lower dimensional space.

Description

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(s)

C.A.Kapourani [e-mail]

andreaskapou/SeuratPipe documentation built on Nov. 22, 2022, 4:16 p.m.