pFlowMerge: Parellel call to flowMerge

In RGLab/flowMerge: Cluster Merging for Flow Cytometry Data

Description

Calls the flowMerge methods to compute the merged solution from a flowClust object or set of objects in a parallelized manner using the snow framework.

Usage

pFlowMerge(flowData, cl, K = 1:15, B.init = 100, tol.init = 0.01, tol = 1e-05, B = 500, randomStart = 10, nu = 4, nu.est = 0, trans = 1, varNames = NA)

Arguments

flowData	The data to be fit. A list of flowFrames, a flowSet or a flowFrame
cl	The snow cluster object. Can be NULL to call the non-parallel version of flowClust
K	See flowClust documentation
B.init	See flowClust documentation
tol.init	See flowClust documentation
tol	See flowClust documentation
B	See flowClust documentation
randomStart	See flowClust documentation
nu	See flowClust documentation
nu.est	See flowClust documentation
trans	See flowClust documentation
varNames	See flowClust documentation

Details

Makes a parallelized call to flowClust. Parses the results to extract the max BIC solution, merges clusters, finds the optimal k-cluster solution using the entropy and returns it. If cl is NULL, a non-parallel call is made to the flowClust function.

Value

A list of flowMerge objects. One per flowFrame passed into the method.

Warning

This function does not do any special memory management. A large data set will likely cause it to run out of memory and start swapping incessantly. If you have lots of data, it's best to feed it piecewise to pFlowClust.

Author(s)

Greg Finak <[e-mail]>

References

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

See Also

pFlowClust,flowClust,merge,snow, fitPiecewiseLinreg

Examples

data(rituximab)
#Parallelized call below:
## Not run: cl<-makeSOCKcluster(rep("finakg@localhost",7))
## Not run: result<-pFlowMerge(rituximab,cl,varNames=c("FSC.H","SSC.H"))
## Not run: plot(result)
#cl<-NULL;
#result<-pFlowMerge(rituximab,cl=NULL,varNames=c("FSC.H","SSC.H"),K=1:8);
#plot(result);

RGLab/flowMerge documentation built on Aug. 10, 2020, 12:52 p.m.