accTest {cyanoFilter}R Documentation

tests the accuracy of several automated gating functions on monoculture flow cytometry experiments.

Description

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.

Usage

accTest(
  fs,
  sfts = c("phytoFilter", "flowClust", "cytometree"),
  channels,
  nrun = 10000,
  ...
)

Arguments

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

Value

a named list containing the following objects;

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")
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)
              )

[Package cyanoFilter version 1.1.1 Index]