PAMClust: Performs PAM clustering on the active assay of the given...

View source: R/object_funcs.R

PAMClustR Documentation

Performs PAM clustering on the active assay of the given Seurat object. Looks for a distance matrix 'dist' in the 'misc' field of the active assay.

Description

Performs PAM clustering on the active assay of the given Seurat object. Looks for a distance matrix 'dist' in the 'misc' field of the active assay.

Usage

PAMClust(pisces.obj, kmin = 2, kmax = 5)

Arguments

pisces.obj

A Seurat object w/ either 'dist' in the 'misc' field or w/ 'scale.data'.

kmin

Minimum number of clusters. Default of 2.

kmax

Maximum number of clusters. Default of 5.

Value

Seurat object with clustering object 'louvain.clust' added to 'misc' field of active assay. And optimal clustering set as 'pisces.cluster' label for active assay.


califano-lab/PISCES documentation built on Jan. 11, 2023, 5:34 a.m.