remove doublets from a flowFrame, using flowStats
Source:R/CytoProcessingStepImplementations.R
removeDoubletsFlowStats.Rd
Wrapper around flowStats::singletGate(). Can apply the flowStats function subsequently on several channel pairs, e.g. (FSC-A, FSC-H) and (SSC-A, SSC-H)
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
- widerGate
a boolean as wider_gate parameter to flowStats::singletGate()
- ...
additional parameters passed to flowStats::singletGate()
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 <-
removeDoubletsFlowStats(ff_c,
areaChannels = c("FSC-A", "SSC-A"),
heightChannels = c("FSC-H", "SSC-H"),
widerGate = TRUE)
#> Warning: replacing previous import ‘flowViz::contour’ by ‘graphics::contour’ when loading ‘flowStats’