merge: Merge clusters in flow cytometry data

In flowMerge: Cluster Merging for Flow Cytometry Data

Description

Merge the clusters in a flowClust solution using the cluster merging algorithm and entropy criterion.

Usage

merge(x,y,...)

Arguments

x	A flowObj object created from a flowClust object and a flowFrame using the flowObj constructor.
y	missing
...	Additional arguments. i.e. metric="entropy"|"mahalanobis"

Details

Run the cluster merging algorithm on the max BIC solution from a call to flowClust. The optional argument, metric specifies the measure used for clustering. Either "mahalanobis" or "entropy". Defaults to "entropy".

Value

A list of unnamed flowMerge objects. The first element of the list corresponds to the 1–cluster merged solution. The second element corresponds to the 2–cluster merged solution, and so on.

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

flowClust,flowObj

Examples

#data(rituximab)
#data(RituximabFlowClustFit)
#o<-flowObj(flowClust.res[[which.max(BIC(flowClust.res))]],rituximab)
#m<-merge(o);

Example output

Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: feature
Loading required package: flowClust

Attaching package: 'flowClust'

The following object is masked from 'package:graphics':

    box

Loading required package: Rgraphviz
Loading required package: grid
Loading required package: foreach
Loading required package: snow

Attaching package: 'snow'

The following objects are masked from 'package:BiocGenerics':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, parApply, parCapply,
    parLapply, parRapply, parSapply

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, clusterSplit, makeCluster, parApply,
    parCapply, parLapply, parRapply, parSapply, splitIndices,
    stopCluster


Attaching package: 'flowMerge'

The following object is masked from 'package:snow':

    checkForRemoteErrors

The following object is masked from 'package:stats':

    BIC

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
4: no DISPLAY variable so Tk is not available 

flowMerge documentation built on Nov. 8, 2020, 8:08 p.m.