flowPeaks {flowPeaks} | R Documentation

## Doing the flowPeaks analysis

### Description

This is the core function in the flowPeaks package. It generates the output of the cluster and information associated with each cluster, which can be used by the function `plot` for visualization

### Usage

    flowPeaks(x,tol=0.1,h0=1,h=1.5)

### Arguments

`x` | a data matrix for the flow cytometry data, it needs to have at least two rows, and the names for each column should be unique. For a flowFrame data, its exprssion matrix slot should be used as x, where only channles of interest are selected (see the example below).
`tol` | The tolerance (between 0 and 1) when neighboring clusters should be considered to be merged
`h0` | The multiplier of the vaiarance matrix S0
`h` | The multiplier of the variance matrix S

### Value

It returns an object of class flowPeaks, which is a list of the following variables:

`peaks.cluster` | An integer shows the cluster labels (between 1 and K for K clusters) for each cell. The clustering is based on the flowPeaks algorithm
`peaks` | A summary of the cluster information. It is a list with the following three variables: cid: cluster labels, should always be 1:K; w: the weights of the K clusters; mu: The mean of all cells in the K clusters; S: The variance matrix of the K clusters. Note that each variance matrix for each cluster has been stacked as a column vector
`kmeans.cluster` | An integer shows the cluster labels for the initial kmeans clustering
`kmeans` | A summary of the initial kmeans clustering. The meaning of the variables can be seens in the description of peaks above
`info` | The information that can be used for plot, and how the initial kmeans clustering and the final flowPeaks clustering are connected
`x` | The input data x

### Author(s)

Yongchao Ge yongchao.ge@gmail.com

### References

Ge Y. et al, flowPeaks: a fast unsupervised clustering for flow cytometry data via K-means and density peak finding, 2012, Bioinformatics 8(15):2052-8

### See Also

`plot.flowPeaks`

### Examples

    ##demonstrate how to use a flowFrame
    ## Not run:
    require(flowCore)
    samp <- read.FCS(system.file("extdata","0877408774.B08",
    package="flowCore"))
    ##do the clustering based on the asinh transforamtion of
    ##the first two FL channels
    fp<-flowPeaks(asinh(samp@exprs[,3:4]))
    plot(fp)

    ## End(Not run)

    data(barcode)
    fp<-flowPeaks(barcode[,c(1,3)])
    plot(fp)

    ##to compare it with the gold standard
    evalCluster(barcode.cid,fp$peaks.cluster,method="Vmeasure")

    #to remove the outliers
    fpc<-assign.flowPeaks(fp,fp$x)
    plot(fp,classlab=fpc,drawboundary=FALSE,
      drawvor=FALSE,drawkmeans=FALSE,drawlab=TRUE)

    #to adjust the cluster by increasing the tol,h0, h, which results
    #in a smaller number of clusters
    fp2<-adjust.flowPeaks(fp,tol=0.5,h0=2,h=2)
    summary(fp2)
    print(fp) #an alternative of using summary(fp)

[Package flowPeaks version 1.40.0 Index]