runKNN: Calculate k-nearest neighbors of CYT

In JhuangLab/CytoTree: A Toolkit for Flow And Mass Cytometry Data

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

JhuangLab/CytoTree documentation built on Nov. 16, 2020, 7:23 a.m.