runKNN {CytoTree}R Documentation

Calculate k-nearest neighbors of CYT

Description

Calculates and stores a k-nearest neighbor graph based on Euclidean distance with (KMKNN) algorithm using log-transformed signaling matrix of flow cytometry data. The base function are base on findKNN.

Usage

runKNN(
  object,
  given.mat = NULL,
  knn = 30,
  knn.replace = TRUE,
  verbose = FALSE,
  ...
)

Arguments

object

an CYT object

given.mat

matrix. Given matrix to run knn

knn

numeric. Number of k-nearest neighbors.

knn.replace

logic. Whether to replace knn in CYT object

verbose

logical. Whether to print calculation progress.

...

Parameters passing to findKNN function

Value

An CYT object with knn, knn.index and knn.distance information.

See Also

findKNN


[Package CytoTree version 1.2.0 Index]