accTest {cyanoFilter} | R Documentation |
This function gates all flowFrames in the supplied flowSet to attach cluster labels. Then it mixes up the flowSet into one giant flowFrame and re-gates this to attach another label. These labels are used to examine if the gating algorithms can reproduce the earlier clusters before the mixing.
accTest( fs, sfts = c("phytoFilter", "flowClust", "cytometree"), channels, nrun = 10000, ... )
fs |
flowSet with each flowFrame being a phytoplankton monoculture FCM experiment |
sfts |
character vector of gating function to test. |
channels |
channels to be used for gating |
nrun |
number of times the resampling should be done |
... |
extra options to be parsed to the gating function |
a named list containing the following objects;
depth - the multivariate-depth (median) of each flowFrame in the flowset supplied
accuracy - computed accuracy based on resampling after joining the flowFrames together.
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) #phytoFilter specification gateFunc(flowfile = reducedFlowframe(cells_nodebris), channels = c("RED.B.HLin", "YEL.B.HLin", "RED.R.HLin", "FSC.HLin", "SSC.HLin"), sfts = "phytoFilter", list(ph = 0.1, proportion = 0.90) )