remove debris from a flowFrame using manual gating

remove debris from a flowFrame, using manual gating in the FSC-A, SSC-A 2D representation. The function internally uses flowCore::polygonGate()

removeDebrisManualGate(ff, FSCChannel, SSCChannel, gateData, ...)

Arguments

ff

a flowCore::flowFrame

FSCChannel

a character containing the exact name of the forward scatter channel

SSCChannel

a character containing the exact name of the side scatter channel

gateData

a numerical vector containing the polygon gate coordinates first the FSCChannel channel coordinates of each points of the polygon gate, then the SSCChannel channel coordinates of each points.

...

additional parameters passed to flowCore::polygonGate()

Value

a flowCore::flowFrame with removed debris events from the input

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")        
#> Compensating file : Donor2.fcs


remDebrisGateData <- c(73615, 110174, 213000, 201000, 126000,
                       47679, 260500, 260500, 113000, 35000)

ff_cells <-
    removeDebrisManualGate(ff_c,
                           FSCChannel = "FSC-A",
                           SSCChannel = "SSC-A",
                           gateData = remDebrisGateData)