labelCluster: Label each cluster as "+" or "-" or neutral for each marker
In MetaCyto: MetaCyto: A package for meta-analysis of cytometry data

Description Usage Arguments Value Examples

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

1 2	labelCluster(fcsFrame, clusterList, excludeClusterParameters = c("TIME"), minPercent = 0.05, labelQuantile = 0.95, cutoff = NULL)

`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.

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.

# 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"))