remove doublets from a flowFrame, using PeacoQC

wrapper around PeacoQC::RemoveDoublets(). Can apply the PeacoQC function subsequently on several channel pairs, e.g. (FSC-A, FSC-H) and (SSC-A, SSC-H)

Usage

removeDoubletsPeacoQC(
  ff,
  areaChannels,
  heightChannels,
  nmads = rep(4, length(areaChannels)),
  verbose = TRUE,
  ...
)

Arguments

ff

a flowCore::flowFrame

areaChannels

a character vector containing the name of the 'area type' channels one wants to use

heightChannels

a character vector containing the name of the 'height type' channels one wants to use

nmads

a numeric vector with the bandwidth above the ratio allowed, per channels pair (cells are kept if the ratio between -A channel[i] and -H channel[i] is smaller than the median ratio + nmad[i] times the median absolute deviation of the ratios). Default is 4, for all channel pairs.

verbose

If set to TRUE, the median ratio and width will be printed.

...

additional parameters passed to PeacoQC::RemoveDoublets()

Value

a flowCore::flowFrame with removed doublets 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_s <-
    removeDoubletsPeacoQC(ff_c,
                          areaChannels = c("FSC-A", "SSC-A"),
                          heightChannels = c("FSC-H", "SSC-H"),
                          nmads = c(3, 5))                            
#> Median ratio: 1.11051333489904, width: 0.146677138600654
#> Median ratio: 1.07502856441465, width: 0.15333572575707