this function is a wrapper around flowClean::clean() function. It also pre-selects the channels to be handled (=> all signal channels)
Usage
qualityControlFlowClean(
ff,
preTransform = FALSE,
transList = NULL,
outputDiagnostic = FALSE,
outputDir = NULL,
verbose = TRUE,
...
)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
- outputDiagnostic
if TRUE, stores diagnostic files generated by flowClean in outputDir directory
- outputDir
used in conjunction with outputDiagnostic
- verbose
if TRUE messages comments on the QC process
- ...
additional parameters passed to flowClean::clean()
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)
ff_QualityControl <- suppressWarnings(
qualityControlFlowClean(fsRaw[[2]],
binSize = 0.01, # default
nCellCutoff = 500, # default
cutoff = "median", # default
fcMax = 1.3, # default
nstable = 5))
#> Applying flowClean method...
#> [1] "flowClean detected too few cells in /__w/_temp/Library/CytoPipeline/extdata/Donor2.fcs."