flowMatch-package {flowMatch} | R Documentation

## Matching cell populations and building meta-clusters and templates from a collection of FC samples.

### Description

Matching cell populations and building meta-clusters and templates from a collection of FC samples.

### Details

Package: | flowMatch
Type: | Package
Version: | 1.0
Date: | 2013-08-01
License: | GPL (>= 2)
LazyLoad: | yes

### Author(s)

Ariful Azad <aazad@purdue.edu>

### References

Azad, Ariful and Pyne, Saumyadipta and Pothen, Alex (2012), Matching phosphorylation response patterns of antigen-receptor-stimulated T cells via flow cytometry; BMC Bioinformatics, 13 (Suppl 2), S10.

Azad, Ariful and Langguth, Johannes and Fang, Youhan and Qi, Alan and Pothen, Alex (2010), Identifying rare cell populations in comparative flow cytometry; Algorithms in Bioinformatics, Springer, 162-175.

### Examples

    ## ------------------------------------------------
    ## load data
    ## ------------------------------------------------

    library(healthyFlowData)
    data(hd)

    ## ------------------------------------------------
    ## Retrieve each sample, clsuter it and store the
    ## clustered samples in a list
    ## ------------------------------------------------
    set.seed(1234) # for reproducable clustering
    cat('Clustering samples: ')
    clustSamples = list()
    for(i in 1:length(hd.flowSet))
    {
      cat(i, ' ')
      sample1 = exprs(hd.flowSet[[i]])
      clust1 = kmeans(sample1, centers=4, nstart=20)
      cluster.labels1 = clust1$cluster
      clustSample1 = ClusteredSample(labels=cluster.labels1, sample=sample1)
      clustSamples = c(clustSamples, clustSample1)
    }

    ## ------------------------------------------------
    ## Create a template from the list of clustered samples and plot functions
    ## ------------------------------------------------

    template = create.template(clustSamples)
    summary(template)

    ## plot the tree denoting the hierarchy of the samples in a template
    tree = template.tree(template)

    ## plot the template in terms of the meta-clusters
    ## option-1 (default): plot contours of each cluster of the meta-clusters
    plot(template)

[Package flowMatch version 1.16.0 Index]