flowMerge (version 2.20.0)

flowMerge-package: Merging of mixture components for automated gating of flow cytometry data.

Description

Merges mixture components from the flowClust framework based on the entropy of clustering and provides a simple representation of complicated, non-convex cell populations.

Details

Package:

flowMerge

Type:

Package

Version:

0.4.1

Date:

2009-09-07

License:

Artistic-2.0

LazyLoad:

yes

Depends:

methods

High density, non-convex cell populations in flow cytometry data often require multiple mixture components for a good model fit. The components are often overlapping, resulting in a complicated representation of individual cell populations. flowMerge merges overlapping mixture components (based on the max BIC flowClust model fit) in an iterative manner based on an entropy criterion, allowing these cell populations to be represented by individual mixture components while retaining the good model fitting properties of the BIC solution. Estimates of the number of clusters from a flowMerge model more accurately represent the "true" number of cell populations in the data. Running flowMerge is relatively straightforward. A flowClust object is converted to a flowObj object, which groups the model and the data (a flowFrame) into a single object. This is done by a call to flowObj(model, data) with a call to merge, which takes a flowObj object. The algorithm may be run in parallel on a multi-core machine or a networked cluster of machines. It uses the functionality in the snow package to achieve this. Parallelized calls to flowClust are available via the pFlowClust and pFlowMerge functions.

flowMerge has functionality to automatically select the "correct" number of clusters by fitting a piecewise linear model to the entropy of clustering vs number of clusters, and locating the position of the changepoint. The piecewise linear model fitting is invoked by a call to fitPiecewiseLinreg, which returns the location of the changepoint.

References

Finak G, Bashasharti A, Brinkmann R, Gottardo R. Merging Mixture Model Components for Improved Cell Population Identification in High Throughput Flow Cytometry Data; Advances in Bioinformatics (To Appear)

See Also

flowClust,flowObj,pFlowMerge,pFlowClust,fitPiecewiseLinreg,merge,getData,link{plot}

Examples

#data(rituximab)
#data(RituximabFlowClustFit)
#o<-flowObj(flowClust.res[[which.max(flowMerge:::BIC(flowClust.res))]],rituximab);
#m<-merge(o);
#i<-fitPiecewiseLinreg(m);
#m<-m[[i]];
#plot(m,pch=20,level=0.9);