clusterExtract {cyanoFilter}R Documentation

extract clusters based on supplied cluster indicator

Description

extract clusters based on supplied cluster indicator

Usage

clusterExtract(flowfile, cluster_var = "Clusters", cluster_val = NULL)

Arguments

flowfile

flowframe containing cluster indicators as well

cluster_var

column name in expression matrix containing the cluter indicators, cannot be NULL.

cluster_val

cluster number, cannot be NULL.

Value

flowFrame containing the clusters

Examples


flowfile_path <- system.file("extdata", "B4_18_1.fcs", 
                             package = "cyanoFilter",
                             mustWork = TRUE)
flowfile <- flowCore::read.FCS(flowfile_path, alter.names = TRUE,
                               transformation = FALSE, emptyValue = FALSE,
                               dataset = 1) 
flowfile_nona <- cyanoFilter::noNA(x = flowfile)
flowfile_noneg <- cyanoFilter::noNeg(x = flowfile_nona)
flowfile_logtrans <- cyanoFilter::lnTrans(x = flowfile_noneg, 
                                         c('SSC.W', 'TIME'))
cells_nonmargin <- cellMargin(flowframe = flowfile_logtrans, 
                              Channel = 'SSC.W',
           type = 'estimate', y_toplot = "FSC.HLin")
fin <- phytoFilter(flowfile = reducedFlowframe(cells_nonmargin),
              pig_channels = c("RED.B.HLin", "YEL.B.HLin", "RED.R.HLin"),
              com_channels = c("FSC.HLin", "SSC.HLin"))

clusterExtract(flowfile = reducedFlowframe(fin),
    cluster_var = "Clusters",
    cluster_val = 1)


[Package cyanoFilter version 1.1.1 Index]