perform QC with flowAI — qualityControlFlowAI • CytoPipeline

this function is a wrapper around flowAI::flow_auto_qc() function. It also pre-selects the channels to be handled (=> all signal channels)

Usage

qualityControlFlowAI(
  ff,
  preTransform = FALSE,
  transList = NULL,
  outputDiagnostic = FALSE,
  outputDir = NULL,
  ...
)

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 flowAI in outputDir directory
outputDir: used in conjunction with outputDiagnostic
...: additional parameters passed to flowAI::flow_auto_qc()

Value

a flowCore::flowFrame with removed low quality 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_QualityControl <- 
    qualityControlFlowAI(fsRaw[[2]],
                         remove_from = "all", # all default
                         second_fractionFR = 0.1,
                         deviationFR = "MAD",
                         alphaFR = 0.01,
                         decompFR = TRUE,
                         outlier_binsFS = FALSE,
                         pen_valueFS = 500,
                         max_cptFS = 3,
                         sideFM = "both",
                         neg_valuesFM = 1))
#> Applying flowAI method...
#> Quality control for the file: Donor2
#> 66.42% of anomalous cells detected in the flow rate check. 
#> 0% of anomalous cells detected in signal acquisition check. 
#> 0.1% of anomalous cells detected in the dynamic range check.