clusters-methods: description of function clusters

In stela2502/StefansExpressionSet: StefansExpressionSet

description of function clusters

Description

Culters the data either based on the raw data values or any MDS data type and adds the grouping into the samples table.

Usage

clusters(dataObj, clusterby = "raw", useGrouping = NULL, groups.n = 3,
  ctype = "hierarchical clust", onwhat = "Expression",
  cmethod = "ward.D2", name = NULL)

Arguments

dataObj	the StefansExpressionSet object
clusterby	cluster on raw data or MDS clustered data default="raw"
useGrouping	do nothing and simply use tis grouping default=NULL
groups.n	how many groups should be detected default= 3
ctype	cluster type - either 'hierarchical clust' or 'kmeans' default = 'hierarchical clust'
onwhat	this option has been kept for the Fluidigm data as there FACS data can also be used default = 'Expression'
cmethod	the method to used with the hclust clustering (default = 'ward.D2')
name	the name for the new grouping (default = 'auto_clusters.1:n')

stela2502/StefansExpressionSet documentation built on April 24, 2023, 8:15 p.m.