run.clustering: Clustering the data

In rezakj/scSeqR: scSeqR; a toolkit to analyze single cell sequencing data types (i.e scRNA-seq) and large numeric matrix files.

Clustering the data

Description

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

Usage

run.clustering(x = NULL, clust.method = "kmeans",
  dist.method = "euclidean", index.method = "silhouette",
  max.clust = 25, min.clust = 2, dims = 1:10)

Arguments

x	An object of class scSeqR.
clust.method	the cluster analysis method to be used. This should be one of: "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", "centroid", "kmeans".
dist.method	the distance measure to be used to compute the dissimilarity matrix. This must be one of: "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski" or "NULL". By default, distance="euclidean". If the distance is "NULL", the dissimilarity matrix (diss) should be given by the user. If distance is not "NULL", the dissimilarity matrix should be "NULL".
index.method	the index to be calculated. This should be one of : "kl", "ch", "hartigan", "ccc", "scott", "marriot", "trcovw", "tracew", "friedman", "rubin", "cindex", "db", "silhouette", "duda", "pseudot2", "beale", "ratkowsky", "ball", "ptbiserial", "gap", "frey", "mcclain", "gamma", "gplus", "tau", "dunn", "hubert", "sdindex", "dindex", "sdbw", "all" (all indices except GAP, Gamma, Gplus and Tau), "alllong" (all indices with Gap, Gamma, Gplus and Tau included).
max.clust	maximal number of clusters, between 2 and (number of objects - 1), greater or equal to min.nc.
min.clust	minimum number of clusters, defult = 2.
dims	PCA dimentions to be use for clustering, defult = 1:10.

Value

An object of class scSeqR.

Examples

## Not run: 
my.obj <- run.clustering(my.obj,
                        clust.method = "kmeans",
                        dist.method = "euclidean",
                        index.method = "silhouette",
                        max.clust = 25,
                        min.clust = 2,
                        dims = 1:10)

## End(Not run)

rezakj/scSeqR documentation built on March 28, 2022, 12:17 p.m.