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]