Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/clusterDistances.R
Compute the dissimilarity between a pair of FC templates by using Mixed Edge Cover (MEC) algorithm.
1 | dist.template(template1, template2, dist.type='Mahalanobis', unmatch.penalty=999999)
|
template1 |
an object of class |
template2 |
an object of class |
dist.type |
character, indicating the method with which the dissimilarity between a pair of meta-clusters is computed. Supported dissimilarity measures are: 'Mahalanobis', 'KL' and 'Euclidean'. |
unmatch.penalty |
A numeric value denoting the penalty for leaving a meta-cluster unmatched. This parameter should be already known or be estimated empirically estimated from data (see the reference for a discussion). Default is set to a very high value so that no meta-cluster remains unmatched. |
We used a robust version of matching called Mixed Edge Cover (MEC) to match meta-clusters across a pair of templates. MEC allows a meta-cluster to be matched with zero, one or more than one meta-clusters in a paired template. The cost of an MEC solution is equal to the summation of dissimilarities of the matched meta-clusters and penalty for the unmatched meta-clusters. The MEC algorithm finds an optimal solution by minimizing the cost of MEC, which is then used as dissimilarity between a pair of templates.
dist.template
returns a numeric value representing dissimilarity between a pair of templates. This value is equal to the summation of dissimilarities of the matched meta-clusters and penalty for the unmatched meta-clusters.
Ariful Azad
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | ## ------------------------------------------------
## load data and retrieve two templates
## ------------------------------------------------
library(healthyFlowData)
data(hd)
## ------------------------------------------------
## Retrieve each sample, clsuter it and store the
## clustered samples in a list
## ------------------------------------------------
cat('Clustering samples: ')
clustSamples = list()
for(i in 1:10) # read 10 samples and cluster them
{
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 two templates each from five samples
## ------------------------------------------------
template1 = create.template(clustSamples[1:5])
template2 = create.template(clustSamples[6:10])
D = dist.template(template1, template2, dist.type='Mahalanobis', unmatch.penalty=999999)
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