summaries {cyanoFilter} | R Documentation |
takes a flowframes, a vector of channels, cluster indicator and return desired summaries per cluster
summaries(object, channels, cluster_var, summary)
object |
An object of class cyanoFilter to be summarised. |
channels |
channels whose summaries are to be computed |
cluster_var |
column name in expression matrix containing the cluter indicators |
summary |
summary statistic of interest. Only mean and variance-covariance matrix supported at the moment. |
list containing computed summaires
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") cells_nodebris <- debrisNc(flowframe = reducedFlowframe(cells_nonmargin), ch_chlorophyll = "RED.B.HLin", ch_p2 = "YEL.B.HLin", ph = 0.05)