NENT: Extract the Normalized Entropy

In flowMerge: Cluster Merging for Flow Cytometry Data

Description

Extracts the normalized entropy from a list of flowMerge objects.

Usage

NENT(x)

Arguments

x	A list of flowMerge objects

Details

The normalized entropy is extracted from a flowMerge object by computing \frac{E}{K*n} where E is the entropy, and K and n are the number of clusters and data points, respectively.

Value

Returns a vector of normalized entropy values for the flowMerge objects.

Warning

This function doesn't do enough error checking and will try to extract the entropy from a list of anything.

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; Advances in Bioinformatics (To Appear)

See Also

ENT,merge,flowMerge-class

Examples

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

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, cbind, colMeans, colSums, colnames, 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.