remove debris from a flowFrame, using flowClust

this function removes debris from a flowFrame, using clustering capabilities of flowClust::tmixFilter(). The idea is to pre-select a number of clusters to be found in the (FSC,SSC) 2D view, and select all clusters behalve the one closest nearest the origin. Then we take all events that are inside the probaLevel quantile curve for at least one of the remaining clusters.

Usage

removeDebrisFlowClust(
  ff,
  FSCChannel,
  SSCChannel,
  nClust,
  probaLevel = 0.9,
  ...
)

Arguments

ff

a flowCore::flowFrame

FSCChannel

the name of the FSC channel

SSCChannel

the name of the SSC channel

nClust

number of clusters to identify

probaLevel

the probability level

...

additional parameters passed to flowClust::flowClust()

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")        


ff_cells <-
    removeDebrisFlowClust(ff_c,
                          FSCChannel = "FSC-A",
                          SSCChannel = "SSC-A",
                          nClust = 3,
                          probaLevel = 0.9,
                          B = 100)
#> Using the serial version of flowClust