find_neighbors: K Nearest Neighbour Search

In robustSingleCell: Robust Clustering of Single Cell RNA-Seq Data

Description

Uses a kd-tree to find the p number of near neighbours for each point in an input/output dataset.

Usage

find_neighbors(data, k)

Arguments

data	matrix; input data matrix
k	integer; number of nearest neighbours

Details

Use the nn2 function from the RANN package, utilizes the Approximate Near Neighbor (ANN) C++ library, which can give the exact near neighbours or (as the name suggests) approximate near neighbours to within a specified error bound. For more information on the ANN library please visit http://www.cs.umd.edu/~mount/ANN/.

Value

a n-by-k matrix of neighbor indices

Examples

iris_unique <- unique(iris) # Remove duplicates
data <- as.matrix(iris_unique[,1:4])
neighbors <- find_neighbors(data, k=10)

robustSingleCell documentation built on May 2, 2019, 2:11 p.m.