clusterStats {MetaCyto} | R Documentation |
A function that derives summary statistics for clusters.
clusterStats(fcsFrame, clusterList, fcsNames)
fcsFrame |
A flow Frame object returned from preprocessing function. Must contain a parameter called "sample_id" that specify the origin of each cell using integer IDs. |
clusterList |
A list, each element should be a vector containing the IDs of all cells that belong to a cluster. |
fcsNames |
A vector of fcs file names. Each element corresponds to an integer ID in the "sample_id" parameter in fcsFrame. |
Returns a data frame, rows correspond to each fcs file, columns correspond to MFI of markers or fractions.
# Find fcs files files=system.file("extdata","SDY420/ResultFiles/CyTOF_result", package="MetaCyto") files=list.files(files,pattern="fcs$",full.names=TRUE) # Preprocess fcs = preprocessing(fcsFiles=files,assay ="CyTOF",b=1/8) # Search clusters cluster_list=searchCluster(fcsFrame=fcs, clusterLabel=c("CD3+|CD8+","CD3-|CD19+")) # derive summary statistics cluster_stats=clusterStats(fcsFrame=fcs, clusterList=cluster_list$clusterList, fcsNames=files)