MetaClustering {FlowSOM}R Documentation

MetaClustering

Description

Cluster data with automatic number of cluster determination for several algorithms

Usage

MetaClustering(data, method, max = 20, nClus = NULL, ...)

Arguments

data

Matrix containing the data to cluster

method

Clustering method to use, given as a string. Options are metaClustering_consensus,metaClustering_hclust, metaClustering_kmeans,metaClustering_som

max

Maximum number of clusters to try out

nClus

Exact number of clusters to use. If not NULL, max will be ignored.

...

Extra parameters to pass along

Value

Numeric array indicating cluster for each datapoint

See Also

metaClustering_consensus

Examples

   # Read from file, build self-organizing map and minimal spanning tree
   fileName <- system.file("extdata","lymphocytes.fcs",package="FlowSOM")
   flowSOM.res <- ReadInput(fileName, compensate=TRUE,transform=TRUE,
                            scale=TRUE)
   flowSOM.res <- BuildSOM(flowSOM.res,colsToUse=c(9,12,14:18))
   flowSOM.res <- BuildMST(flowSOM.res)
   
   # Apply metaclustering
   metacl <- MetaClustering(flowSOM.res$map$codes,
                            "metaClustering_consensus",
                            max=10)
   
   # Get metaclustering per cell
   flowSOM.clustering <- metacl[flowSOM.res$map$mapping[,1]]
[Package FlowSOM version 1.14.1 Index]