run.phenograph {iCellR}

Clustering the data

Description

This function takes an object of class iCellR and finds optimal number of clusters and clusters the data.

Usage

run.phenograph(x = NULL, k = 100, data.type = "pca", dims = 1:10)

Arguments

x

An object of class iCellR.

k

integer; number of nearest neighbours (default:45)

data.type

Choose between "tsne", "pca", "umap", default = "pca".

dims

PCA dimentions to be use for clustering, default = 1:10.

Value

An object of class iCellR.