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

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

See Also

findKNN


[Package CytoTree version 1.0.3 Index]