remove dead cells from a flowFrame

this function removes dead cells from a flowFrame, using a specific '(a)live/dead' channel, and the flowDensity::deGate() gating function (see doc of the flowDensity package)

Usage

removeDeadCellsDeGate(
  ff,
  preTransform = FALSE,
  transList = NULL,
  LDMarker,
  keepPositivePop = FALSE,
  ...
)

Arguments

ff

a flowCore::flowFrame

preTransform

if TRUE, apply the transList scale transform prior to running the gating algorithm

transList

applied in conjunction with preTransform == TRUE

LDMarker

a character containing the exact name of the marker corresponding to Live/Dead channel, or the Live/Dead channel name itself

keepPositivePop

logical flag stating whether we want to keep, after gating, the population that is positive for LDMarker (TRUE) or negative for LDmarker (FALSE)

...

additional parameters passed to flowDensity::deGate()

Value

a flowCore::flowFrame with removed dead cells from the input

Details

rawDataDir <- system.file("extdata", package = "CytoPipeline") sampleFiles <- file.path(rawDataDir, list.files(rawDataDir, pattern = "Donor"))

Examples

rawDataDir <- system.file("extdata", package = "CytoPipeline")
sampleFiles <-
    file.path(rawDataDir, list.files(rawDataDir, pattern = "Donor"))

truncateMaxRange <- FALSE
minLimit <- NULL

# create flowCore::flowSet with all samples of a dataset
fsRaw <- readSampleFiles(
    sampleFiles = sampleFiles,
    whichSamples = "all",
    truncate_max_range = truncateMaxRange,
    min.limit = minLimit)

suppressWarnings(ff_m <- removeMarginsPeacoQC(x = fsRaw[[2]]))
#> Removing margins from file : Donor2.fcs
    
ff_c <-
    compensateFromMatrix(ff_m,
                         matrixSource = "fcs")        

transList <- 
    estimateScaleTransforms(        
        ff = ff_c,
        fluoMethod = "estimateLogicle",
        scatterMethod = "linear",
        scatterRefMarker = "BV785 - CD3")

ff_lcells <-
    removeDeadCellsDeGate(ff_c,
                          preTransform = TRUE,
                          transList = transList,
                          LDMarker = "L/D Aqua - Viability",
                          keepPositivePop = FALSE)
#> Removing Dead Cells events (using flowDensity::deGate()) from file : Donor2.fcs