flowSOM.MC {MetaCyto} | R Documentation |
A function that cluster cytometry data using FlowSOM.
flowSOM.MC(fcsFrame, excludeClusterParameters, xdim = 10, ydim = 10, k = 40, seed = NULL)
fcsFrame |
A flow frame. |
excludeClusterParameters |
A vector specifying the name of markers not to be used for clustering. |
xdim |
An integer, defines the width of SOM |
ydim |
An integer, defines the height of SOM |
k |
An integer, defines the number of clusters to be identified by flowSOM. |
seed |
Set seed for reproducible results. |
A list of clusters. Each cluster contains the ID of all cells that belong to the cluster.
# 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"))