labelCluster {MetaCyto} | R Documentation

## Label each cluster as "+" or "-" or neutral for each marker

### Description

A function that labels each cluster as "+" or "-" or neutral for each marker

### Usage

    labelCluster(fcsFrame, clusterList, excludeClusterParameters = c("TIME"),
      minPercent = 0.05, labelQuantile = 0.95, cutoff = NULL)

### Arguments

`fcsFrame` | A flowFrame object.
`clusterList` | A list, each element should be a vector containing the IDs of all cells that belongs to a cluster
`excludeClusterParameters` | A vector specifying the name of markers not to be used for labeling.
`minPercent` | A number between 0 and 0.5. Used to specify the minimum percent of cells in the positive and negative region after bisection. Keep it small to avoid bisecting uni-mode distributions.
`labelQuantile` | A number between 0.5 and 1. Used to specify the minimum percent of a cluster required to be larger or smaller than the cutoff value for labeling.
`cutoff` | A vector of cutoff values to bisect the distribution of each marker. The names of the vector should be the same as the marker names. If NULL, the cutoff value will be determined automatically.

### Value

Returns a list with two components: 1) clusterLabel, contains a vector of labels, each corresponds to a cluster in clusterList. 2) cutoff, contains a vector of cutoff values used to bisect each marker.

### Examples

    # Find fcs files
    files=system.file("extdata","SDY420/ResultFiles/CyTOF_result",
                      package="MetaCyto")
    files=list.files(files,pattern="fcs$",full.names=TRUE)
    # Preprocess
    fcs = preprocessing(fcsFiles=files,assay ="CyTOF",b=1/8)
    # cluster using flowSOM.MC
    cluster_list=flowSOM.MC(fcsFrame=fcs,
                            excludeClusterParameters=c("Time","Cell_length"))
    # label each clusters
    cluster_label=labelCluster(fcsFrame=fcs,clusterList=cluster_list,
                               excludeClusterParameters=c("Time","Cell_length"))

[Package MetaCyto version 1.2.1 Index]